SMTL ID : 6u6c.1 (1 other biounit)

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK2-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

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

FMT.1: 5 residues within 4Å: Chain A: V.38, G.83, R.85, R.87, D.88 Ligand excluded by PLIP FMT.2: 6 residues within 4Å: Chain A: Y.30, E.57, M.106, Y.181, I.237 Ligands: MLI.11 Ligand excluded by PLIP FMT.3: 4 residues within 4Å: Chain A: L.113, G.116, V.117, Q.144 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: D.140, R.168, A.171 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain A: R.11, L.130 Ligand excluded by PLIP FMT.7: 4 residues within 4Å: Chain A: G.69, P.70, T.71, S.240 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: M.67, M.106, L.159 Ligand excluded by PLIP FMT.9: 5 residues within 4Å: Chain A: Y.30, V.60, D.68, M.106, Y.108 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain A: T.165 Chain B: A.36, E.39, E.40 Ligand excluded by PLIP FMT.17: 1 residues within 4Å: Chain B: H.81 Ligand excluded by PLIP FMT.19: 4 residues within 4Å: Chain B: S.311, H.312, S.313, D.319 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain B: D.274, D.343, W.403 Ligand excluded by PLIP FMT.24: 3 residues within 4Å: Chain B: G.334, D.337 Ligands: FMT.30 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain B: R.164, G.167, A.168 Chain D: L.406 Ligand excluded by PLIP FMT.26: 6 residues within 4Å: Chain B: R.155, Q.156, I.314, A.316, D.396, T.399 Ligand excluded by PLIP FMT.27: 4 residues within 4Å: Chain B: D.57, L.110, R.113 Ligands: EPE.39 Ligand excluded by PLIP FMT.29: 1 residues within 4Å: Chain B: R.265 Ligand excluded by PLIP FMT.30: 6 residues within 4Å: Chain B: R.265, L.266, R.335, D.337 Ligands: FMT.24, FMT.31 Ligand excluded by PLIP FMT.31: 3 residues within 4Å: Chain B: P.262, R.265 Ligands: FMT.30 Ligand excluded by PLIP FMT.32: 6 residues within 4Å: Chain B: A.287, G.288, S.289, L.300, L.301, Q.302 Ligand excluded by PLIP FMT.33: 2 residues within 4Å: Chain B: R.119, N.194 Ligand excluded by PLIP FMT.34: 1 residues within 4Å: Chain B: R.60 Ligand excluded by PLIP FMT.35: 2 residues within 4Å: Chain B: R.77, Q.80 Ligand excluded by PLIP FMT.36: 2 residues within 4Å: Chain B: S.51, D.53 Ligand excluded by PLIP FMT.40: 5 residues within 4Å: Chain B: R.164, L.165 Chain D: G.351, R.355, L.406 Ligand excluded by PLIP FMT.43: 3 residues within 4Å: Chain B: P.71, Q.229 Ligands: FMT.54 Ligand excluded by PLIP FMT.45: 5 residues within 4Å: Chain C: P.162, A.198, E.201, L.202, R.205 Ligand excluded by PLIP FMT.47: 4 residues within 4Å: Chain C: K.207, A.208, S.210, D.211 Ligand excluded by PLIP FMT.48: 3 residues within 4Å: Chain C: E.151, H.152, R.153 Ligand excluded by PLIP FMT.52: 8 residues within 4Å: Chain C: L.137, I.138, P.139, F.158, L.159, R.168, T.172 Chain D: E.32 Ligand excluded by PLIP FMT.54: 7 residues within 4Å: Chain B: P.69, S.70, P.71 Chain D: A.63, G.67, R.68 Ligands: FMT.43 Ligand excluded by PLIP FMT.55: 4 residues within 4Å: Chain B: A.138, L.166, G.167 Chain D: R.355 Ligand excluded by PLIP FMT.56: 3 residues within 4Å: Chain C: P.65 Chain D: N.185, R.189 Ligand excluded by PLIP FMT.58: 3 residues within 4Å: Chain D: K.47, E.48, R.114 Ligand excluded by PLIP FMT.59: 5 residues within 4Å: Chain D: R.155, H.312, S.313, D.319 Ligands: FMT.67 Ligand excluded by PLIP FMT.60: 1 residues within 4Å: Chain D: W.403 Ligand excluded by PLIP FMT.61: 4 residues within 4Å: Chain C: Q.144 Chain D: S.23, G.24, F.297 Ligand excluded by PLIP FMT.62: 4 residues within 4Å: Chain D: V.267, D.337, R.339, E.378 Ligand excluded by PLIP FMT.64: 7 residues within 4Å: Chain B: G.358, I.360 Chain D: H.96, T.97, T.135, R.162, L.166 Ligand excluded by PLIP FMT.65: 4 residues within 4Å: Chain D: R.236, L.237, P.238, G.263 Ligand excluded by PLIP FMT.66: 2 residues within 4Å: Chain D: H.11, L.259 Ligand excluded by PLIP FMT.67: 8 residues within 4Å: Chain D: G.273, D.274, R.280, H.312, S.313, I.314, D.343 Ligands: FMT.59 Ligand excluded by PLIP FMT.68: 2 residues within 4Å: Chain D: R.60, L.140 Ligand excluded by PLIP FMT.69: 1 residues within 4Å: Chain D: E.39 Ligand excluded by PLIP FMT.73: 4 residues within 4Å: Chain D: G.141, L.142, D.143 Ligands: EDO.41 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: Y.35, P.36, A.78 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.36, A:A.78 EDO.15: 5 residues within 4Å: Chain B: V.171, A.172, V.173, Q.174, E.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.174, B:T.175 EDO.21: 6 residues within 4Å: Chain B: R.236, L.237, P.238, D.239, G.263, V.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.236 Water bridges: B:L.237, B:G.263 EDO.22: 6 residues within 4Å: Chain B: D.59, Q.62, A.63, R.68, I.221, E.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.59, B:E.225 EDO.23: 5 residues within 4Å: Chain B: A.36, E.40, K.117, A.195, D.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.117, B:A.195 EDO.28: 2 residues within 4Å: Chain B: K.402, G.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.402 EDO.38: 3 residues within 4Å: Chain B: D.274, T.342, S.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.274 Water bridges: B:S.344 EDO.41: 5 residues within 4Å: Chain B: R.355 Chain D: A.138, L.166 Ligands: K.70, FMT.73 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Water bridges: D:L.142, D:D.143 Hydrogen bonds: B:R.355 EDO.44: 4 residues within 4Å: Chain C: G.116, V.117, D.118, A.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.117, C:D.118, C:A.119 Water bridges: C:D.118, C:Q.144 EDO.46: 8 residues within 4Å: Chain C: Y.30, G.59, V.60, D.68, T.76, M.106, Y.108 Ligands: K.51 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.30, C:D.68 EDO.49: 9 residues within 4Å: Chain C: Y.30, E.57, D.68, I.72, M.106, Y.181, I.237 Ligands: MLI.50, K.51 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.57, C:D.68 Water bridges: C:D.68 EDO.63: 4 residues within 4Å: Chain D: D.14, H.18, G.21, P.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.18, D:P.22 EDO.72: 5 residues within 4Å: Chain D: P.262, G.263, V.264, R.265, R.335 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.264, D:R.265, D:R.335

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

ACT.10: 6 residues within 4Å: Chain A: P.162, S.163, S.164, T.165, P.166, R.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.163 Salt bridges: A:R.205 ACT.12: 4 residues within 4Å: Chain A: L.113, Q.144 Chain B: S.23, F.297 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.297 Water bridges: B:Y.29

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

MLI.11: 9 residues within 4Å: Chain A: Y.181, G.217, L.218, G.219, I.237, V.238, G.239, S.240 Ligands: FMT.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.181, A:G.219, A:G.239, A:S.240 Water bridges: A:L.218, A:S.240, A:A.241 MLI.50: 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: EDO.49 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.181, C:G.219, C:V.220, C:I.237, C:G.239, C:S.240 Water bridges: C:S.240, C:A.241

2 x PZV: 1-(2-fluorobenzene-1-carbonyl)-N-methyl-2,3-dihydro-1H-indole-5-sulfonamide(Non-covalent)

PZV.13: 21 residues within 4Å: Chain A: Y.62, D.64, P.65, G.66, M.67, Y.108, D.136 Chain B: Y.29, V.30, P.31, I.184, N.185, F.188, W.191, Y.200, F.202, G.207, P.208, F.211, H.294, G.295 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.188, B:Y.200, B:F.202, B:F.211 pi-Stacking: B:F.188, B:F.202 Hydrogen bonds: A:G.66, A:M.67, A:D.136 Water bridges: A:W.109 PZV.53: 20 residues within 4Å: Chain C: Y.62, D.64, G.66, M.67, Y.108, D.136 Chain D: Y.29, V.30, P.31, L.34, I.184, N.185, F.188, W.191, Y.200, F.202, G.207, P.208, H.294, G.295 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.188, D:Y.200, D:F.202 pi-Stacking: D:F.188, D:F.202 Hydrogen bonds: C:G.66, C:M.67, C:D.136 Water bridges: C:W.109

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

P1T.14: 23 residues within 4Å: Chain B: S.99, H.100, K.101, T.124, G.125, A.126, G.127, Q.128, H.129, 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 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: 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.57: 23 residues within 4Å: Chain D: S.99, H.100, K.101, T.124, G.125, A.126, G.127, Q.128, H.129, 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 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: 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

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 6 residues within 4Å: Chain B: E.40, A.43, A.44, K.47, E.48, R.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.40, B:K.47, B:R.114

5 x K: POTASSIUM ION(Non-covalent)

K.37: 6 residues within 4Å: Chain B: V.245, G.246, A.282, T.284, Y.320, G.322 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.284, B:Y.320, H2O.7, H2O.10 K.51: 4 residues within 4Å: Chain C: D.68, M.106 Ligands: EDO.46, EDO.49 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.68, H2O.16 K.70: 6 residues within 4Å: Chain D: C.137, A.138, L.142, C.144, G.167 Ligands: EDO.41 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:L.142, H2O.19, H2O.19 K.71: 3 residues within 4Å: Chain D: F.293, S.296, S.298 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:F.293, D:S.296, D:S.296, H2O.19 K.74: 2 residues within 4Å: Chain D: E.74, Q.233 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.39: 8 residues within 4Å: Chain B: R.60, L.61, R.113, L.139 Chain D: Y.73, T.76, R.77 Ligands: FMT.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.73, D:Y.73 Water bridges: D:R.77 EPE.42: 8 residues within 4Å: Chain B: G.351, R.355, F.404, L.406 Chain D: R.164, L.165, A.168, E.169 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.164, D:L.165 Water bridges: D:V.170 Salt bridges: B:R.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase. Protein Sci. (2020)

Release Date

2020-09-02

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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