6UB9

Crystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND BRD6309-BOUND FORM

PDB DOI: 10.2210/pdb6UB9/pdb
Entry: 6UB9 supersedes: 6DUA

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

Deposited: 2019-09-11 Released: 2019-09-25
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: 2.78 Å
R-Value Free: 0.210
R-Value Work: 0.169
R-Value Observed: 0.170

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 - AMINOACRYLATE- AND BRD6309-BOUND FORM

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)

To be published.

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
Protein Feature View Expand
Reference Sequence

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(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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 8 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 DA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth H] SDF format, chain X [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain X [auth D]	DA [auth F], M [auth B], MA [auth H], X [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		Ligand Interaction
P1T Query on P1T Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain L [auth B] SDF format, chain LA [auth H] SDF format, chain W [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth H] MOL2 format, chain W [auth D]	CA [auth F], L [auth B], LA [auth H], W [auth D]	2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID C₁₁ H₁₅ N₂ O₇ P BXUDKFHCAMQSRX-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain Z [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain Z [auth D]	IA [auth F], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain NA [auth H] SDF format, chain Y [auth D] SDF format, chain N [auth B] MOL2 format, chain EA [auth F] MOL2 format, chain NA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain N [auth B]	EA [auth F], N [auth B], NA [auth H], Y [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Ligand Interaction
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain U [auth C] SDF format, chain BA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain BA [auth E]	BA [auth E], HA [auth F], J [auth A], JA [auth G], U [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain PA [auth H] MOL2 format, chain PA [auth H]	PA [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain O [auth B] SDF format, chain OA [auth H] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain RA [auth H] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain RA [auth H]	AA [auth E], FA [auth F], GA [auth F], I [auth A], K [auth A], AA [auth E], FA [auth F], GA [auth F], I [auth A], K [auth A], KA [auth H], O [auth B], OA [auth H], P [auth B], Q [auth B], QA [auth H], RA [auth H], S [auth B], T [auth B], V [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Ligand Interaction