SMTL ID : 6u6c.2 (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

1 x ALA: ALANINE(Non-covalent)

ALA.1: 5 residues within 4Å: Chain A: R.223, A.227, A.262, G.263, R.265 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.227 Hydrogen bonds: A:R.265, A:R.265

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

MLI.2: 8 residues within 4Å: Chain A: Y.181, G.217, L.218, G.219, I.237, V.238, G.239, S.240 6 PLIP interactions: 6 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 MLI.32: 4 residues within 4Å: Chain B: S.79, Q.80, S.84, R.381 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.80, B:S.84, B:S.84, B:G.382 Salt bridges: B:R.381 MLI.46: 8 residues within 4Å: Chain C: Y.181, G.217, L.218, G.219, V.238, G.239, S.240 Ligands: FMT.36 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.181, C:G.219, C:I.237, C:G.239, C:S.240 Water bridges: C:V.220, C:V.220, C:A.241 MLI.78: 3 residues within 4Å: Chain D: K.402, W.403, G.405 No protein-ligand interaction detected (PLIP)

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

FMT.3: 5 residues within 4Å: Chain A: G.69, P.70, T.71, I.72, S.240 Ligand excluded by PLIP FMT.4: 5 residues within 4Å: Chain A: Y.30, V.60, D.68, M.106, Y.108 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: Q.144 Chain B: Y.29, F.297 Ligand excluded by PLIP FMT.9: 2 residues within 4Å: Chain B: V.171, E.186 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain B: G.351, R.355 Chain D: L.165 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain B: K.47, E.48, R.114 Ligand excluded by PLIP FMT.15: 5 residues within 4Å: Chain B: R.265, L.266, R.335, D.337 Ligands: EDO.24 Ligand excluded by PLIP FMT.16: 6 residues within 4Å: Chain B: F.293, S.296, S.298, Y.299, G.322, V.323 Ligand excluded by PLIP FMT.18: 2 residues within 4Å: Chain B: R.227, A.257 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain B: E.345, D.348, A.349, A.370, K.374 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain B: H.81, L.373, K.374, V.377 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain B: E.40, K.117, A.195, D.196 Ligand excluded by PLIP FMT.22: 3 residues within 4Å: Chain A: P.65 Chain B: N.185, R.189 Ligand excluded by PLIP FMT.25: 3 residues within 4Å: Chain B: L.237, P.238, G.263 Ligand excluded by PLIP FMT.26: 2 residues within 4Å: Chain B: R.60, L.140 Ligand excluded by PLIP FMT.28: 6 residues within 4Å: Chain B: A.66, G.67, P.69, S.70, L.94, N.95 Ligand excluded by PLIP FMT.29: 2 residues within 4Å: Chain B: D.260, D.261 Ligand excluded by PLIP FMT.33: 8 residues within 4Å: Chain B: H.96, T.97, T.135, R.162, L.166 Chain D: G.358, I.360 Ligands: FMT.49 Ligand excluded by PLIP FMT.36: 7 residues within 4Å: Chain C: Y.30, E.57, I.72, M.106, Y.181, I.237 Ligands: MLI.46 Ligand excluded by PLIP FMT.37: 2 residues within 4Å: Chain C: P.39, V.42 Ligand excluded by PLIP FMT.38: 2 residues within 4Å: Chain C: P.70, R.74 Ligand excluded by PLIP FMT.39: 3 residues within 4Å: Chain C: E.77, L.80, R.81 Ligand excluded by PLIP FMT.40: 5 residues within 4Å: Chain C: K.207, A.208, V.209, S.210, D.211 Ligand excluded by PLIP FMT.41: 5 residues within 4Å: Chain C: G.69, P.70, T.71, I.72, S.240 Ligand excluded by PLIP FMT.42: 4 residues within 4Å: Chain C: A.161, S.163 Chain D: A.33, V.192 Ligand excluded by PLIP FMT.43: 3 residues within 4Å: Chain C: L.146, A.147, E.150 Ligand excluded by PLIP FMT.49: 8 residues within 4Å: Chain B: H.96 Chain D: R.91, D.93, L.94, I.359, I.360, R.392 Ligands: FMT.33 Ligand excluded by PLIP FMT.51: 1 residues within 4Å: Chain D: D.53 Ligand excluded by PLIP FMT.55: 4 residues within 4Å: Chain C: S.63 Chain D: K.181, T.308, E.310 Ligand excluded by PLIP FMT.56: 8 residues within 4Å: Chain D: Q.156, I.314, S.315, A.316, I.363, E.364, K.395, D.396 Ligand excluded by PLIP FMT.57: 3 residues within 4Å: Chain D: R.119, N.194, N.197 Ligand excluded by PLIP FMT.58: 4 residues within 4Å: Chain D: A.172, V.173, Q.174, E.186 Ligand excluded by PLIP FMT.59: 4 residues within 4Å: Chain D: R.113, G.116, K.117, L.142 Ligand excluded by PLIP FMT.62: 7 residues within 4Å: Chain D: G.273, D.274, R.280, H.312, S.313, I.314, D.343 Ligand excluded by PLIP FMT.63: 8 residues within 4Å: Chain B: D.93, L.94, R.392 Chain D: N.95, H.96, T.97, G.98, R.392 Ligand excluded by PLIP FMT.64: 2 residues within 4Å: Chain D: A.333, G.334 Ligand excluded by PLIP FMT.65: 3 residues within 4Å: Chain B: L.406 Chain D: R.164, A.168 Ligand excluded by PLIP FMT.66: 3 residues within 4Å: Chain D: E.74, F.88, Q.233 Ligand excluded by PLIP FMT.67: 6 residues within 4Å: Chain D: F.269, R.339, G.371, K.374, L.375 Ligands: FMT.70 Ligand excluded by PLIP FMT.70: 4 residues within 4Å: Chain D: R.339, P.340, K.374 Ligands: FMT.67 Ligand excluded by PLIP FMT.71: 4 residues within 4Å: Chain D: R.236, L.237, P.238, G.263 Ligand excluded by PLIP FMT.72: 5 residues within 4Å: Chain D: D.274, G.275, E.277, T.342 Ligands: EDO.68 Ligand excluded by PLIP FMT.73: 4 residues within 4Å: Chain D: R.265, L.266, R.335, D.337 Ligand excluded by PLIP FMT.74: 4 residues within 4Å: Chain D: K.331, D.337, Y.338 Ligands: FMT.76 Ligand excluded by PLIP FMT.75: 1 residues within 4Å: Chain D: F.297 Ligand excluded by PLIP FMT.76: 4 residues within 4Å: Chain D: D.337, Y.338, R.339 Ligands: FMT.74 Ligand excluded by PLIP FMT.77: 3 residues within 4Å: Chain D: A.6, D.217, R.220 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: M.67, D.68, M.106, Y.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68 EDO.17: 4 residues within 4Å: Chain B: H.18, G.21, P.22, G.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.143 EDO.24: 5 residues within 4Å: Chain B: P.262, R.265, G.334, R.335 Ligands: FMT.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.335 EDO.27: 3 residues within 4Å: Chain B: A.157, L.158, A.161 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.157, B:A.161 EDO.45: 4 residues within 4Å: Chain C: R.122, A.125, A.126, H.152 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.126, C:H.152 Water bridges: C:R.122, C:E.151 EDO.47: 8 residues within 4Å: Chain C: Y.30, V.60, P.61, Y.62, P.65, D.68, T.76, Y.108 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.30, C:Y.62, C:Y.62 EDO.53: 4 residues within 4Å: Chain D: A.44, 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 EDO.60: 3 residues within 4Å: Chain C: R.85 Chain D: D.303, D.305 No protein-ligand interaction detected (PLIP) EDO.68: 6 residues within 4Å: Chain D: G.273, D.274, T.342, D.343, S.344 Ligands: FMT.72 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.342, D:D.343, D:S.344, D:S.344 Water bridges: D:G.273, D:D.343 EDO.69: 3 residues within 4Å: Chain D: L.259, A.333, R.335 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.259 EDO.81: 3 residues within 4Å: Chain D: R.77, Q.80, M.356 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.77, D:Q.80, D:Q.80

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 3 residues within 4Å: Chain B: R.86, R.236, G.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.86, B:R.86, B:R.236 PGE.14: 6 residues within 4Å: Chain B: S.15, R.28, E.39, T.42, A.43, Q.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.28 Water bridges: B:R.28

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

PZV.7: 21 residues within 4Å: Chain A: Y.62, D.64, G.66, M.67, Y.108, D.136 Chain B: Y.29, V.30, P.31, L.34, I.184, N.185, F.188, W.191, Y.200, F.202, G.207, P.208, F.211, H.294, G.295 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.66, A:M.67, A:D.136, A:D.136 Water bridges: A:W.109 Hydrophobic interactions: B:F.188, B:Y.200, B:F.202, B:F.211 pi-Stacking: B:F.188, B:F.202 PZV.50: 21 residues within 4Å: Chain C: Y.62, D.64, P.65, G.66, M.67, Y.108, D.136 Chain D: 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 D, 4 interactions with chain C Hydrophobic interactions: D:F.188, D:Y.200, D:F.202, D:F.211 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.10: 22 residues within 4Å: Chain B: 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 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.362, B:E.364 Hydrogen bonds: B:K.101, B:G.125, B:A.126, B:G.127, B:Q.128, B:H.129, B:G.246, B:G.247, B:G.248, B:S.249, B:N.250, B:N.250, B:S.390 Water bridges: B:T.204, B:T.204, B:G.248, B:A.251 Salt bridges: B:H.100, B:K.101, B:K.101 pi-Stacking: B:H.100 P1T.52: 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:G.125, D:A.126, D:G.127, D:Q.128, D:H.129, D:T.204, D:G.246, D:G.248, D:S.249, D:S.249, D:N.250, D:N.250, D:S.390 Water bridges: D:G.247, D:G.247, D:G.248, D:A.251 Salt bridges: D:H.100, D:K.101, D:K.101 pi-Stacking: D:H.100

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

ACT.13: 3 residues within 4Å: Chain B: R.119, N.194, N.197 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.197 Salt bridges: B:R.119 ACT.23: 7 residues within 4Å: Chain B: I.151, R.155, R.280, S.311, H.312, S.313, D.319 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.151 Hydrogen bonds: B:R.280, B:S.313 Salt bridges: B:R.155, B:H.312 ACT.54: 4 residues within 4Å: Chain C: L.113, Q.144 Chain D: S.23, F.297 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.113 Water bridges: C:E.141, C:Q.144, D:Y.29

1 x NA: SODIUM ION(Non-functional Binders)

NA.30: 4 residues within 4Å: Chain B: G.67, P.69 Chain D: G.67, P.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.69

3 x K: POTASSIUM ION(Non-covalent)

K.31: 5 residues within 4Å: Chain B: G.246, A.282, T.284, Y.320, G.322 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.284, B:Y.320, B:G.322, H2O.6 K.48: 3 residues within 4Å: Chain C: E.94, A.126, A.127 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.94, C:A.126 K.79: 5 residues within 4Å: Chain D: G.246, A.282, T.284, Y.320, G.322 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.284, D:Y.320, D:G.322, H2O.21

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

PEG.34: 9 residues within 4Å: Chain B: R.77, R.355 Chain D: C.137, A.138, G.141, L.142, D.143, L.166 Ligands: PEG.61 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.143 PEG.44: 4 residues within 4Å: Chain C: A.91, E.94, A.95, I.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.91, C:A.95 PEG.61: 10 residues within 4Å: Chain D: A.134, C.137, A.138, L.142, D.143, C.144, L.166, G.167, A.168 Ligands: PEG.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.138, D:C.144

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

EPE.35: 9 residues within 4Å: Chain B: R.164, L.165, A.168, E.169 Chain D: G.351, C.354, R.355, F.404, L.406 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:L.165, B:A.168, D:R.355 Water bridges: B:V.170, D:R.355 Salt bridges: D:R.355 EPE.80: 7 residues within 4Å: Chain B: Y.73, T.76, R.77 Chain D: L.61, R.113, L.139, L.140 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.113, D:L.140 Water bridges: D:R.60, D:N.64

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
E

C
G

B
F

D
H

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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