SMTL ID : 5tcg.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 10 residues within 4Å: Chain A: Y.181, G.217, L.218, G.219, V.220, I.237, V.238, G.239, S.240 Ligands: FMT.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.181, A:G.219, A:V.220, A:G.239, A:S.240 MLI.11: 10 residues within 4Å: Chain C: Y.181, G.217, L.218, G.219, V.220, I.237, V.238, G.239, S.240 Ligands: FMT.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.181, C:G.219, C:V.220, C:I.237, C:G.239, C:S.240

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

FMT.2: 7 residues within 4Å: Chain A: Y.30, E.57, I.72, M.106, Y.181, I.237 Ligands: MLI.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.57 FMT.6: 3 residues within 4Å: Chain B: K.47, E.48, R.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.47, B:E.48 FMT.7: 4 residues within 4Å: Chain B: G.351, R.355, F.404 Chain D: L.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.355 FMT.8: 3 residues within 4Å: Chain B: R.77, Q.80, M.356 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.77, B:Q.80 FMT.9: 4 residues within 4Å: Chain B: L.165 Chain D: G.351, R.355, F.404 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:L.165, D:R.355 FMT.10: 4 residues within 4Å: Chain B: S.79, Q.80, S.84, R.381 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.381 Water bridges: B:S.84, B:S.84 FMT.12: 7 residues within 4Å: Chain C: Y.30, E.57, I.72, M.106, Y.181, I.237 Ligands: MLI.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.57 FMT.17: 5 residues within 4Å: Chain C: L.113, Q.144 Chain D: S.23, Y.29, F.297 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:G.24, D:Y.29 Hydrogen bonds: C:Q.144 FMT.18: 3 residues within 4Å: Chain D: K.47, E.48, R.114 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.47, D:E.48, D:E.48 FMT.19: 5 residues within 4Å: Chain D: I.151, R.155, H.312, S.313, D.319 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.155, D:S.313, D:S.313 FMT.20: 4 residues within 4Å: Chain D: A.36, E.40, A.195, D.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.40

2 x P1T: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID(Non-covalent)

P1T.3: 24 residues within 4Å: Chain B: S.99, H.100, K.101, T.124, G.125, A.126, G.127, Q.128, H.129, L.180, T.204, C.244, V.245, G.246, G.247, G.248, S.249, N.250, G.317, L.318, A.362, E.364, S.390, G.391 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.180, B:A.362, B:E.364 Hydrogen bonds: B:K.101, B:T.124, B:G.125, B:A.126, B:G.127, B:Q.128, B:H.129, B:T.204, B:G.246, B:G.247, B:G.248, B:S.249, B:S.249, B:N.250, B:N.250, B:S.390 Water bridges: B:G.248, B:A.251 Salt bridges: B:H.100, B:K.101, B:K.101 pi-Stacking: B:H.100 P1T.13: 24 residues within 4Å: Chain D: S.99, H.100, K.101, T.124, G.125, A.126, G.127, Q.128, H.129, L.180, T.204, C.244, V.245, G.246, G.247, G.248, S.249, N.250, G.317, L.318, A.362, E.364, S.390, G.391 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:L.180, D:A.362, D:E.364 Hydrogen bonds: D:K.101, D:T.124, D:G.125, D:A.126, D:G.127, D:Q.128, D:H.129, D:T.204, D:G.246, D:G.247, D:G.248, D:S.249, D:S.249, D:N.250, D:N.250, D:S.390 Water bridges: D:G.248, D:A.251 Salt bridges: D:H.100, D:K.101, D:K.101 pi-Stacking: D:H.100

5 x CS: CESIUM ION(Non-covalent)

CS.4: 6 residues within 4Å: Chain B: V.245, G.246, A.282, T.284, Y.320, G.322 No protein-ligand interaction detected (PLIP) CS.5: 2 residues within 4Å: Chain B: K.402, W.403 No protein-ligand interaction detected (PLIP) CS.14: 6 residues within 4Å: Chain D: V.245, G.246, A.282, T.284, Y.320, G.322 No protein-ligand interaction detected (PLIP) CS.15: 2 residues within 4Å: Chain D: C.137, L.142 No protein-ligand interaction detected (PLIP) CS.16: 4 residues within 4Å: Chain B: G.67, P.69 Chain D: G.67, P.69 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:G.67, B:G.67, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wellington, S. et al., A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase. Nat. Chem. Biol. (2017)

Release Date

2017-05-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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