6UB9 | pdb_00006ub9

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

PDB DOI: https://doi.org/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 (Depositor), 0.208 (DCC)
R-Value Work:
0.169 (Depositor), 0.173 (DCC)
R-Value Observed:
0.170 (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

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.

Macromolecule Content

Total Structure Weight: 292.44 kDa
Atom Count: 19,666
Modeled Residue Count: 2,598
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 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] mmCIF format, chain DA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth H] mmCIF 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		Interactions Focus chain DA [auth F] Focus chain M [auth B] Focus chain MA [auth H] Focus chain X [auth D] Interactions & Density Focus chain DA [auth F] Focus chain M [auth B] Focus chain MA [auth H] Focus chain X [auth D]
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] mmCIF format, chain CA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth H] mmCIF 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		Interactions Focus chain CA [auth F] Focus chain L [auth B] Focus chain LA [auth H] Focus chain W [auth D] Interactions & Density Focus chain CA [auth F] Focus chain L [auth B] Focus chain LA [auth H] Focus chain W [auth D]
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] mmCIF format, chain IA [auth F] mmCIF format, chain Z [auth D]	IA [auth F], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Focus chain Z [auth D] Interactions & Density Focus chain IA [auth F] Focus chain Z [auth D]
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth H] SDF format, chain Y [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain EA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain Y [auth D]	EA [auth F], N [auth B], NA [auth H], Y [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain N [auth B] Focus chain NA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth F] Focus chain N [auth B] Focus chain NA [auth H] Focus chain Y [auth D]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain HA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain U [auth C] MOL2 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] mmCIF format, chain BA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain U [auth C]	BA [auth E], HA [auth F], J [auth A], JA [auth G], U [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain JA [auth G] Focus chain U [auth C] Interactions & Density Focus chain BA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain JA [auth G] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain PA [auth H] MOL2 format, chain PA [auth H] mmCIF format, chain PA [auth H]	PA [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain PA [auth H] Interactions & Density Focus chain PA [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
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 RA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] 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 RA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C]	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		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.210 (Depositor), 0.208 (DCC)
R-Value Work: 0.169 (Depositor), 0.173 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.373	α = 90
b = 159.619	β = 90
c = 164.932	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
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: 2019-09-25

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

This entry supersedes: 6DUA

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

Revision History (Full details and data files)

Version 1.0: 2019-09-25
Type: Initial release
Version 1.1: 2019-10-30
Changes: Advisory, Data collection
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description