6UAP | pdb_00006uap

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound

PDB DOI: https://doi.org/10.2210/pdb6UAP/pdb
Entry: 6UAP supersedes: 6DU1

Classification: Lyase/Lyase Inhibitor
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-11 Released: 2019-10-30
Deposition Author(s): Chang, C., Michalska, K., Maltseva, N.I., Jedrzejczak, R., McCarren, P., Nag, P.P., Joachimiak, A., Satchell, K., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): Structure-guided Drug Discovery Coalition

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.171 (Depositor), 0.174 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound

Chang, C., Michalska, K., Maltseva, N.I., Jedrzejczak, R., McCarren, P., Nag, P.P., Joachimiak, A., Satchell, K.

To be published.

Macromolecule Content

Total Structure Weight: 292.44 kDa
Atom Count: 19,739
Modeled Residue Count: 2,604
Deposited Residue Count: 2,744
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A, C, E, G	276	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpA, Rv1613, MTCY01B2.05 EC: 4.2.1.20
UniProt
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFY1 Go to UniProtKB: P9WFY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFY1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B, D, F, H	410	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpB, Rv1612, MTCY01B2.04 EC: 4.2.1.20
UniProt
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX9 Go to UniProtKB: P9WFX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H9V (Subject of Investigation/LOI) Query on H9V Download:Ideal Coordinates CCD File SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain UA [auth H] SDF format, chain W [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain W [auth D] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain W [auth D]	KA [auth F], L [auth B], UA [auth H], W [auth D]	(2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile C₁₇ H₁₂ Cl F₃ N₂ XHUZEPHBFHVYMY-YQQAZPJKSA-N		Interactions Focus chain KA [auth F] Focus chain L [auth B] Focus chain UA [auth H] Focus chain W [auth D] Interactions & Density Focus chain KA [auth F] Focus chain L [auth B] Focus chain UA [auth H] Focus chain W [auth D]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain P [auth B] SDF format, chain QA [auth F] SDF format, chain WA [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain WA [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain WA [auth H]	FA [auth D], GA [auth D], P [auth B], QA [auth F], WA [auth H]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain P [auth B] Focus chain QA [auth F] Focus chain WA [auth H] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain P [auth B] Focus chain QA [auth F] Focus chain WA [auth H]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain PA [auth F] SDF format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain U [auth C]	O [auth B], PA [auth F], U [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain PA [auth F] Focus chain U [auth C] Interactions & Density Focus chain O [auth B] Focus chain PA [auth F] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain K [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain K [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain K [auth A]	HA [auth D], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain K [auth A] Interactions & Density Focus chain HA [auth D] Focus chain K [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain TA [auth G] SDF format, chain X [auth D] SDF format, chain XA [auth H] SDF format, chain Y [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain TA [auth G] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain TA [auth G] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth D]	IA [auth D] JA [auth D] TA [auth G] X [auth D] XA [auth H] IA [auth D], JA [auth D], TA [auth G], X [auth D], XA [auth H], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain IA [auth D] Focus chain JA [auth D] Focus chain TA [auth G] Focus chain X [auth D] Focus chain XA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain IA [auth D] Focus chain JA [auth D] Focus chain TA [auth G] Focus chain X [auth D] Focus chain XA [auth H] Focus chain Y [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth H] SDF format, chain Z [auth D] SDF format, chain YA [auth H] SDF format, chain DA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth H] mmCIF format, chain DA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], I [auth A], J [auth A], LA [auth F], M [auth B], MA [auth F], N [auth B], NA [auth F], OA [auth F], Q [auth B], R [auth B], RA [auth F], S [auth B], SA [auth G], T [auth C], V [auth C], VA [auth H], YA [auth H], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth C] Focus chain V [auth C] Focus chain VA [auth H] Focus chain YA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth C] Focus chain V [auth C] Focus chain VA [auth H] Focus chain YA [auth H] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	B, D, F, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.211 (Depositor), 0.214 (DCC)
R-Value Work: 0.171 (Depositor), 0.174 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.777	α = 90
b = 157.877	β = 90
c = 166.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

This entry supersedes: 6DU1

Funding Organization	Location	Grant Number
Structure-guided Drug Discovery Coalition	Canada	--

Revision History (Full details and data files)

Version 1.0: 2019-10-30
Type: Initial release
Version 1.1: 2025-04-02
Changes: Advisory, Data collection, Database references, Structure summary