SMTL ID : 6uap.1 (1 other biounit)

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-2-2-mer

Ligands

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: M.67, M.106, A.183 No protein-ligand interaction detected (PLIP) FMT.2: 4 residues within 4Å: Chain A: Y.30, V.60, D.68, Y.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.30, A:V.60 FMT.5: 4 residues within 4Å: Chain A: Q.144 Chain B: S.23, Y.29, F.297 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.144, B:Y.29 FMT.6: 4 residues within 4Å: Chain B: R.236, L.237, P.238, G.263 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.236 FMT.9: 7 residues within 4Å: Chain B: E.74, A.75, T.76, S.79, A.85, R.86, I.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.74, B:E.74, B:I.87 FMT.10: 4 residues within 4Å: Chain B: A.44, K.47, E.48, R.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.47, B:E.48 FMT.11: 4 residues within 4Å: Chain B: A.36, E.40, A.195, D.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.36, B:E.40 FMT.12: 5 residues within 4Å: Chain C: Y.30, V.60, D.68, M.106, Y.108 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.30, C:M.106 FMT.15: 4 residues within 4Å: Chain D: A.172, V.173, Q.174, E.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.174, D:E.186 FMT.18: 5 residues within 4Å: Chain D: R.236, L.237, P.238, D.239, G.263 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.236, D:D.239

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Y.181, G.217, L.218, G.219, G.239, S.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.181, A:G.239, A:S.240, A:S.240

2 x H9V: (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile(Non-covalent)

H9V.4: 15 residues within 4Å: Chain A: D.64, G.66, Y.108, D.136 Chain B: V.30, P.31, L.34, I.184, N.185, F.188, Y.200, F.202, P.208, F.211, H.294 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.184, B:F.188, B:F.188, B:Y.200, B:P.208 pi-Stacking: B:F.202 Hydrogen bonds: A:G.66, A:D.136 H9V.14: 16 residues within 4Å: Chain C: D.64, G.66, Y.108, D.136 Chain D: V.30, P.31, L.34, I.184, N.185, F.188, W.191, Y.200, F.202, P.208, F.211, H.294 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.66 Hydrophobic interactions: D:I.184, D:F.188, D:W.191, D:Y.200, D:P.208 pi-Stacking: D:F.188, D:F.202

1 x MLA: MALONIC ACID(Non-covalent)

MLA.7: 5 residues within 4Å: Chain B: G.273, D.274, T.342, D.343, S.344 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.343, B:S.344, B:S.344

2 x MLT: D-MALATE(Non-covalent)

MLT.8: 10 residues within 4Å: Chain B: K.101, T.124, G.125, A.126, G.127, Q.128, H.129, A.316, G.317, E.364 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.128 Hydrogen bonds: B:T.124, B:A.126, B:Q.128, B:H.129 Salt bridges: B:K.395 MLT.16: 10 residues within 4Å: Chain D: K.101, T.124, G.125, A.126, G.127, Q.128, H.129, A.316, G.317, E.364 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.126, D:A.316 Hydrogen bonds: D:T.124, D:G.125, D:A.126, D:Q.128, D:H.129 Water bridges: D:N.159 Salt bridges: D:K.395

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 2 residues within 4Å: Chain C: Q.144 Chain D: Y.29 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.144, C:Q.144, D:Y.29 ACT.17: 5 residues within 4Å: Chain D: R.265, L.266, G.334, R.335, D.337 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.266, D:D.337 Water bridges: D:R.335 Salt bridges: D:R.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound. To be Published

Release Date

2019-10-30

Peptides

Tryptophan synthase alpha chain: AC
Tryptophan synthase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
G

B
B

D
H

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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