6UAP

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
R-Value Work: 0.171
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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
Modelled Residue Count: 2,604
Deposited Residue Count: 2,744
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFY1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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 P [auth B] SDF format, chain QA [auth F] SDF format, chain WA [auth H] SDF format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain WA [auth H] MOL2 format, chain GA [auth D]	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]	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]	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]	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 DA [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 YA [auth H] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [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 YA [auth H] MOL2 format, chain Z [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]