7KKG

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KKG/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-10-27 Released: 2021-11-03
Deposition Author(s): Saran, S., Majdi Yazdi, M., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.169 (Depositor), 0.170 (DCC)
R-Value Work:
0.138 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

Saran, S., Majdi Yazd, M., Palmer, D.R.J., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 209.28 kDa
Atom Count: 16,387
Modelled Residue Count: 1,796
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 1 Gene Names: dapA, Cj0806 EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain I [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A]	I [auth A], PA [auth D], S [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain PA [auth D] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain PA [auth D] Focus chain S [auth B]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain HA [auth C] SDF format, chain K [auth A] SDF format, chain IA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth C]	EB [auth F], HA [auth C], IA [auth C], K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EB [auth F] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain K [auth A] Interactions & Density Focus chain EB [auth F] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain K [auth A]
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain HB [auth F] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain ZA [auth E] MOL2 format, chain HB [auth F] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain HB [auth F] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain ZA [auth E]	HB [auth F] LA [auth C] N [auth A] RA [auth D] U [auth B] HB [auth F], LA [auth C], N [auth A], RA [auth D], U [auth B], ZA [auth E]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain HB [auth F] Focus chain LA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain U [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain HB [auth F] Focus chain LA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain U [auth B] Focus chain ZA [auth E]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain DB [auth F] SDF format, chain GA [auth C] SDF format, chain J [auth A] SDF format, chain QA [auth D] SDF format, chain UA [auth E] SDF format, chain T [auth B] SDF format, chain VA [auth E] MOL2 format, chain DB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth E] mmCIF format, chain DB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain VA [auth E]	DB [auth F] GA [auth C] J [auth A] QA [auth D] T [auth B] DB [auth F], GA [auth C], J [auth A], QA [auth D], T [auth B], UA [auth E], VA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DB [auth F] Focus chain GA [auth C] Focus chain J [auth A] Focus chain QA [auth D] Focus chain T [auth B] Focus chain UA [auth E] Focus chain VA [auth E] Interactions & Density Focus chain DB [auth F] Focus chain GA [auth C] Focus chain J [auth A] Focus chain QA [auth D] Focus chain T [auth B] Focus chain UA [auth E] Focus chain VA [auth E]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] mmCIF format, chain FB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E]	FB [auth F] GB [auth F] JA [auth C] KA [auth C] L [auth A] FB [auth F], GB [auth F], JA [auth C], KA [auth C], L [auth A], M [auth A], WA [auth E], XA [auth E], YA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth F] Focus chain GB [auth F] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Interactions & Density Focus chain FB [auth F] Focus chain GB [auth F] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain IB [auth F] SDF format, chain JB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain JB [auth F] mmCIF format, chain IB [auth F] mmCIF format, chain JB [auth F]	IB [auth F], JB [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain IB [auth F] Focus chain JB [auth F] Interactions & Density Focus chain IB [auth F] Focus chain JB [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain BA [auth C] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain P [auth B]	AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth C], AB [auth F], BA [auth C], BB [auth F], CA [auth C], CB [auth F], DA [auth C], G [auth A], MA [auth D], NA [auth D], O [auth B], OA [auth D], P [auth B], Q [auth B], R [auth B], SA [auth E], TA [auth E], W [auth C], X [auth C], Y [auth C], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain G [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain G [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain H [auth A] SDF format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain FA [auth C]	EA [auth C], FA [auth C], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A]