SMTL ID : 6e9p.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-2-2-mer

Ligands

1 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 8 residues within 4Å: Chain A: I.72, Y.181, G.217, L.218, G.219, V.220, G.239, S.240 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.181, A:G.219, A:V.220, A:G.239, A:S.240 Water bridges: A:L.218, A:A.241

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

FMT.2: 4 residues within 4Å: Chain A: G.116, V.117, D.118, A.119 Ligand excluded by PLIP FMT.3: 3 residues within 4Å: Chain A: P.39, V.42, A.43 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: L.113, Q.144 Chain B: S.23, Y.29 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain B: H.11, R.335 Ligand excluded by PLIP FMT.7: 1 residues within 4Å: Chain B: W.403 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain B: H.11, D.12, F.19, G.20, W.329 Ligand excluded by PLIP FMT.9: 2 residues within 4Å: Chain B: N.64 Chain D: Q.233 Ligand excluded by PLIP FMT.10: 1 residues within 4Å: Chain B: Q.80 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain B: R.265, L.266, R.335, D.337 Ligands: EDO.14 Ligand excluded by PLIP FMT.16: 8 residues within 4Å: Chain B: G.291, F.293, S.296, S.298, Y.299, L.300, G.322, V.323 Ligand excluded by PLIP FMT.17: 4 residues within 4Å: Chain B: A.44, K.47, E.48, R.114 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain B: S.23, G.24, E.332 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain B: Y.73, T.76, R.77, E.357 Chain D: L.139 Ligand excluded by PLIP FMT.20: 8 residues within 4Å: Chain B: V.245, G.246, E.270, A.282, T.284, Y.320, G.322, V.323 Ligand excluded by PLIP FMT.23: 2 residues within 4Å: Chain D: S.23, F.297 Ligand excluded by PLIP FMT.24: 1 residues within 4Å: Chain D: E.39 Ligand excluded by PLIP FMT.25: 2 residues within 4Å: Chain D: V.160, V.170 Ligand excluded by PLIP FMT.26: 6 residues within 4Å: Chain D: E.345, D.348, A.349, A.370, L.373, K.374 Ligand excluded by PLIP

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

HDJ.5: 17 residues within 4Å: Chain A: D.64, G.66, M.67, 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, G.295 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.30, B:F.188, B:Y.200, B:Y.200, B:F.202, B:P.208, B:F.211 pi-Stacking: B:F.188, B:F.202 Hydrogen bonds: A:D.64, A:G.66, A:M.67 HDJ.22: 17 residues within 4Å: Chain C: D.64, G.66, M.67, Y.108, D.136 Chain D: V.30, P.31, L.34, I.184, N.185, F.188, Y.200, F.202, P.208, F.211, H.294, G.295 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.30, D:F.188, D:Y.200, D:Y.200, D:F.202, D:P.208, D:F.211 pi-Stacking: D:F.188, D:F.202 Hydrogen bonds: C:D.64, C:G.66

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

EDO.12: 3 residues within 4Å: Chain B: K.402, G.405, N.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.402 EDO.13: 7 residues within 4Å: Chain B: K.101, T.124, G.125, A.126, G.127, Q.128, H.129 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.125, B:A.126, B:G.127, B:Q.128, B:H.129 EDO.14: 5 residues within 4Å: Chain B: P.262, G.263, R.265, R.335 Ligands: FMT.11 No protein-ligand interaction detected (PLIP) EDO.15: 1 residues within 4Å: Chain B: N.409 No protein-ligand interaction detected (PLIP) EDO.21: 6 residues within 4Å: Chain C: Y.181, G.217, G.219, I.237, G.239, S.240 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.181, C:G.217, C:G.219, C:G.239, C:S.240 EDO.27: 3 residues within 4Å: Chain D: P.262, G.263, R.265 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.265, D:R.335 EDO.28: 6 residues within 4Å: Chain B: L.139, L.140 Chain D: Y.73, T.76, R.77, E.357 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.73, D:Y.73, D:T.76 EDO.29: 1 residues within 4Å: Chain D: R.236 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2018-08-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

B
D

D
F

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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