6E9P

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
R-Value Work: 0.176
R-Value Observed: 0.177

Starting Model: experimental
View more details

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

Find similar proteins by:

(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
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]	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]	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 I [auth A] SDF format, chain W [auth C] MOL2 format, chain I [auth A] MOL2 format, chain W [auth C]	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 IB [auth H] 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 V [auth B] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain YA [auth F] 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 IB [auth H] 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 V [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain YA [auth F]	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]	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 SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] 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 SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	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
R-Value Work: 0.176
R-Value Observed: 0.177
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