6E9P | pdb_00006e9p

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD0059 bound

PDB DOI: https://doi.org/10.2210/pdb6E9P/pdb

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

Deposited: 2018-08-01 Released: 2018-08-08
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (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 - closed 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: 292.61 kDa
Atom Count: 19,733
Modelled Residue Count: 2,602
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 LOADING

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 LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDJ Query on HDJ Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CB [auth H] SDF format, chain L [auth B] SDF format, chain RA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain L [auth B] MOL2 format, chain RA [auth F] mmCIF format, chain AA [auth D] mmCIF format, chain CB [auth H] mmCIF format, chain L [auth B] mmCIF format, chain RA [auth F]	AA [auth D], CB [auth H], L [auth B], RA [auth F]	(2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile C₁₈ H₁₅ F₃ N₂ OZFKPHFHTNQIQS-XYJFISCASA-N		Interactions Focus chain AA [auth D] Focus chain CB [auth H] Focus chain L [auth B] Focus chain RA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain CB [auth H] Focus chain L [auth B] Focus chain RA [auth F]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain I [auth A] MOL2 format, chain W [auth C] MOL2 format, chain I [auth A] mmCIF format, chain W [auth C] mmCIF format, chain I [auth A]	I [auth A], W [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain W [auth C] Interactions & Density Focus chain I [auth A] Focus chain W [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain QA [auth E] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain YA [auth F] SDF format, chain IB [auth H] SDF format, chain V [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain QA [auth E] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain IB [auth H] MOL2 format, chain V [auth B] mmCIF format, chain AB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain QA [auth E] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain IB [auth H] mmCIF format, chain V [auth B]	AB [auth G] HA [auth D] HB [auth H] IA [auth D] IB [auth H] AB [auth G], HA [auth D], HB [auth H], IA [auth D], IB [auth H], JA [auth D], K [auth A], KA [auth D], QA [auth E], V [auth B], WA [auth F], XA [auth F], YA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain QA [auth E] Focus chain V [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F] Interactions & Density Focus chain AB [auth G] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain QA [auth E] Focus chain V [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain ZA [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain ZA [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain ZA [auth G]	BB [auth G], J [auth A], O [auth B], Q [auth B], ZA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth G] Focus chain J [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain ZA [auth G] Interactions & Density Focus chain BB [auth G] Focus chain J [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain ZA [auth G]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain JB [auth H] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain VA [auth F] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain SA [auth F] SDF format, chain UA [auth F] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain JB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain SA [auth F] MOL2 format, chain UA [auth F] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain JB [auth H] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain SA [auth F] mmCIF format, chain UA [auth F]	BA [auth D] CA [auth D] DA [auth D] DB [auth H] EA [auth D] BA [auth D], CA [auth D], DA [auth D], DB [auth H], EA [auth D], EB [auth H], FA [auth D], FB [auth H], GA [auth D], GB [auth H], JB [auth H], LA [auth D], MA [auth D], N [auth B], NA [auth D], OA [auth D], P [auth B], PA [auth D], R [auth B], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], VA [auth F], X [auth C], Y [auth C], Z [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain JB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain JB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

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: 2.57 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.66	α = 90
b = 157.944	β = 90
c = 166.078	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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection