MolNFT v1 · #165946 · protein

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and BRD6309-bound form

6UB9 · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and BRD6309-bound form”. X-ray diffraction, 3 ligands (P1T, H9V, CS), 20 pockets (best druggability 0.82). MolNFT v1…

PDB: 6UB9
Type: protein
Length: 2,598 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophan synthase alpha chain; Tryptophan synthase beta chain
EC: 4.2.1.20
UniProt: P9WFY1, P9WFX9
Ligands: P1T, H9V, CS
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryptophan synthase alpha chain (EC 4.2.1.20)	protein	249	50% helix, 15% strand	P9WFY1
B	Tryptophan synthase beta chain (EC 4.2.1.20)	protein	404	47% helix, 20% strand	P9WFX9
C	Tryptophan synthase alpha chain (EC 4.2.1.20)	protein	248	51% helix, 15% strand	P9WFY1
D	Tryptophan synthase beta chain (EC 4.2.1.20)	protein	399	48% helix, 20% strand	P9WFX9
E	Tryptophan synthase alpha chain (EC 4.2.1.20)	protein	247	51% helix, 15% strand	P9WFY1
F	Tryptophan synthase beta chain (EC 4.2.1.20)	protein	400	47% helix, 20% strand	P9WFX9
G	Tryptophan synthase alpha chain (EC 4.2.1.20)	protein	248	51% helix, 15% strand	P9WFY1
H	Tryptophan synthase beta chain (EC 4.2.1.20)	protein	403	44% helix, 19% strand	P9WFX9

Ligands and binding sites

P1T · 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]acrylic acid · ligand · 4 copies · chains B, D, F, H
H9V · (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile · ligand · 4 copies · chains A, B, C, D, E, F, G, H
CS · Cesium ion · metal · 4 copies · chains B, D, F, H
FMT · Formic acid · additive · 15 copies · chains A, B, D, H, C, E, F, G
MLA · Malonic acid · additive · 5 copies · chains A, C, E, F, H, G
PGE · Triethylene glycol · additive · 2 copies · chains D, F
ACT · Acetate ion · additive · chains B
EDO · 1,2-ethanediol · additive · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.82	0.97	29	H9V
2	416	0.82	0.90	54	empty
3	154	0.82	0.97	28	H9V
4	151	0.81	0.97	31	H9V
5	147	0.80	0.96	28	H9V

Interfaces

10 interfaces between chains.

B–D · 1727 Å² buried · 23 hydrogen bonds · protein-protein
F–H · 1722 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1355 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1342 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1317 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

6UB9 · Crystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND… · the same entry in another collection · chain H against H, TM-score 1.00
P9WFY1 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P9WFY1) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P9WFY1
Every structure of UniProt P9WFX9
Elsewhere: RCSB PDB 6UB9 · PDBe 6UB9 · UniProt P9WFY1 · UniProt P9WFX9

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