4H1T | pdb_00004h1t

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

PDB DOI: https://doi.org/10.2210/pdb4H1T/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-11 Released: 2013-09-11
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.217 (Depositor), 0.213 (DCC)
R-Value Work:
0.177 (Depositor), 0.174 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 169.78 kDa
Atom Count: 13,160
Modeled Residue Count: 1,504
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0 Gene Names: udp EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1 Go to UniProtKB: Q9K4U1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K4U1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain UC [auth F] SDF format, chain TC [auth F] SDF format, chain SC [auth F] SDF format, chain SA [auth B] SDF format, chain RC [auth F] SDF format, chain RB [auth D] SDF format, chain RA [auth B] SDF format, chain QC [auth F] SDF format, chain QB [auth D] SDF format, chain QA [auth B] SDF format, chain PC [auth F] SDF format, chain OC [auth F] SDF format, chain JB [auth C] SDF format, chain IB [auth C] SDF format, chain HB [auth C] SDF format, chain GB [auth C] SDF format, chain FB [auth C] SDF format, chain FA [auth A] SDF format, chain EB [auth C] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CC [auth E] SDF format, chain CA [auth A] SDF format, chain BC [auth E] SDF format, chain BA [auth A] SDF format, chain AC [auth E] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain UC [auth F] MOL2 format, chain TC [auth F] MOL2 format, chain SC [auth F] MOL2 format, chain SA [auth B] MOL2 format, chain RC [auth F] MOL2 format, chain RB [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain QC [auth F] MOL2 format, chain QB [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain PC [auth F] MOL2 format, chain OC [auth F] MOL2 format, chain JB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CC [auth E] MOL2 format, chain CA [auth A] MOL2 format, chain BC [auth E] MOL2 format, chain BA [auth A] MOL2 format, chain AC [auth E] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain UC [auth F] mmCIF format, chain TC [auth F] mmCIF format, chain SC [auth F] mmCIF format, chain SA [auth B] mmCIF format, chain RC [auth F] mmCIF format, chain RB [auth D] mmCIF format, chain RA [auth B] mmCIF format, chain QC [auth F] mmCIF format, chain QB [auth D] mmCIF format, chain QA [auth B] mmCIF format, chain PC [auth F] mmCIF format, chain OC [auth F] mmCIF format, chain JB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CC [auth E] mmCIF format, chain CA [auth A] mmCIF format, chain BC [auth E] mmCIF format, chain BA [auth A] mmCIF format, chain AC [auth E] mmCIF format, chain AA [auth A]	AA [auth A] AC [auth E] BA [auth A] BC [auth E] CA [auth A] AA [auth A], AC [auth E], BA [auth A], BC [auth E], CA [auth A], CC [auth E], DA [auth A], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], OC [auth F], PC [auth F], QA [auth B], QB [auth D], QC [auth F], RA [auth B], RB [auth D], RC [auth F], SA [auth B], SC [auth F], TC [auth F], UC [auth F], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AC [auth E] Focus chain BA [auth A] Focus chain BC [auth E] Focus chain CA [auth A] Focus chain CC [auth E] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain SA [auth B] Focus chain SC [auth F] Focus chain TC [auth F] Focus chain UC [auth F] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth E] Focus chain BA [auth A] Focus chain BC [auth E] Focus chain CA [auth A] Focus chain CC [auth E] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain SA [auth B] Focus chain SC [auth F] Focus chain TC [auth F] Focus chain UC [auth F] Focus chain Z [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain UB [auth E] SDF format, chain TB [auth E] SDF format, chain KB [auth D] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain FC [auth F] MOL2 format, chain WA [auth C] MOL2 format, chain UB [auth E] MOL2 format, chain TB [auth E] MOL2 format, chain KB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain FC [auth F] mmCIF format, chain WA [auth C] mmCIF format, chain UB [auth E] mmCIF format, chain TB [auth E] mmCIF format, chain KB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain FC [auth F]	FC [auth F] IA [auth B] JA [auth B] KB [auth D] TB [auth E] FC [auth F], IA [auth B], JA [auth B], KB [auth D], TB [auth E], UB [auth E], WA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FC [auth F] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KB [auth D] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain WA [auth C] Interactions & Density Focus chain FC [auth F] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KB [auth D] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain WA [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain TA [auth C] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain DC [auth F] MOL2 format, chain TA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain DC [auth F] mmCIF format, chain TA [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain DC [auth F]	DC [auth F], GA [auth B], HA [auth B], TA [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DC [auth F] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain TA [auth C] Interactions & Density Focus chain DC [auth F] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain TA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZB [auth E] SDF format, chain ZA [auth C] SDF format, chain YB [auth E] SDF format, chain YA [auth C] SDF format, chain XB [auth E] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WB [auth E] SDF format, chain W [auth A] SDF format, chain VB [auth E] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OB [auth D] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NB [auth D] SDF format, chain N [auth A] SDF format, chain MC [auth F] SDF format, chain MB [auth D] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LC [auth F] SDF format, chain LB [auth D] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KC [auth F] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JC [auth F] SDF format, chain J [auth A] SDF format, chain IC [auth F] SDF format, chain I [auth A] SDF format, chain HC [auth F] SDF format, chain H [auth A] SDF format, chain GC [auth F] SDF format, chain CB [auth C] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain ZB [auth E] MOL2 format, chain ZA [auth C] MOL2 format, chain YB [auth E] MOL2 format, chain YA [auth C] MOL2 format, chain XB [auth E] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WB [auth E] MOL2 format, chain W [auth A] MOL2 format, chain VB [auth E] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MC [auth F] MOL2 format, chain MB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LC [auth F] MOL2 format, chain LB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth F] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JC [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IC [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HC [auth F] MOL2 format, chain H [auth A] MOL2 format, chain GC [auth F] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain ZB [auth E] mmCIF format, chain ZA [auth C] mmCIF format, chain YB [auth E] mmCIF format, chain YA [auth C] mmCIF format, chain XB [auth E] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WB [auth E] mmCIF format, chain W [auth A] mmCIF format, chain VB [auth E] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MC [auth F] mmCIF format, chain MB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LC [auth F] mmCIF format, chain LB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth F] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JC [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IC [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HC [auth F] mmCIF format, chain H [auth A] mmCIF format, chain GC [auth F] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] CB [auth C] GC [auth F] H [auth A] AB [auth C], BB [auth C], CB [auth C], GC [auth F], H [auth A], HC [auth F], I [auth A], IC [auth F], J [auth A], JC [auth F], K [auth A], KA [auth B], KC [auth F], L [auth A], LA [auth B], LB [auth D], LC [auth F], M [auth A], MA [auth B], MB [auth D], MC [auth F], N [auth A], NB [auth D], O [auth A], OA [auth B], OB [auth D], P [auth A], PA [auth B], Q [auth A], S [auth A], T [auth A], U [auth A], V [auth A], VB [auth E], W [auth A], WB [auth E], X [auth A], XA [auth C], XB [auth E], YA [auth C], YB [auth E], ZA [auth C], ZB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain IC [auth F] Focus chain J [auth A] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KC [auth F] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain ZA [auth C] Focus chain ZB [auth E] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain IC [auth F] Focus chain J [auth A] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KC [auth F] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain ZA [auth C] Focus chain ZB [auth E]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain R [auth A] SDF format, chain PB [auth D] SDF format, chain NC [auth F] SDF format, chain NA [auth B] SDF format, chain DB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain R [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain NC [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain DB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain R [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain NC [auth F] mmCIF format, chain NA [auth B] mmCIF format, chain DB [auth C]	DB [auth C] NA [auth B] NC [auth F] PB [auth D] R [auth A] DB [auth C], NA [auth B], NC [auth F], PB [auth D], R [auth A], Y [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain DB [auth C] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain PB [auth D] Focus chain R [auth A] Focus chain Y [auth A] Interactions & Density Focus chain DB [auth C] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain PB [auth D] Focus chain R [auth A] Focus chain Y [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain UA [auth C] MOL2 format, chain UA [auth C] mmCIF format, chain UA [auth C]	UA [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain UA [auth C] Interactions & Density Focus chain UA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain VA [auth C] SDF format, chain EC [auth F] MOL2 format, chain VA [auth C] MOL2 format, chain EC [auth F] mmCIF format, chain VA [auth C] mmCIF format, chain EC [auth F]	EC [auth F], VA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EC [auth F] Focus chain VA [auth C] Interactions & Density Focus chain EC [auth F] Focus chain VA [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain SB [auth E] SDF format, chain G [auth A] MOL2 format, chain SB [auth E] MOL2 format, chain G [auth A] mmCIF format, chain SB [auth E] mmCIF format, chain G [auth A]	G [auth A], SB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain SB [auth E] Interactions & Density Focus chain G [auth A] Focus chain SB [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.217 (Depositor), 0.213 (DCC)
R-Value Work: 0.177 (Depositor), 0.174 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.691	α = 69.62
b = 71.08	β = 72.56
c = 87.937	γ = 85.74

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description