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

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK1-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

hetero-2-2-mer

Ligands

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

FMT.1: 3 residues within 4Å: Chain A: P.36, L.246, T.247 No protein-ligand interaction detected (PLIP) FMT.2: 2 residues within 4Å: Chain A: A.183 Chain B: A.33 No protein-ligand interaction detected (PLIP) FMT.6: 4 residues within 4Å: Chain B: G.351, R.355, L.406 Chain D: L.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.355 FMT.7: 4 residues within 4Å: Chain A: Q.144 Chain B: S.23, F.297 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain B: P.262, V.264, R.265, R.335 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.335 FMT.10: 3 residues within 4Å: Chain B: K.47, E.48, R.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.47 FMT.11: 4 residues within 4Å: Chain B: L.237, P.238, G.263, V.264 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.263 FMT.12: 1 residues within 4Å: Chain B: R.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.189 FMT.22: 1 residues within 4Å: Chain C: Y.115 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.114 FMT.28: 5 residues within 4Å: Chain D: A.172, V.173, Q.174, T.175, E.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.174, D:T.175 FMT.29: 3 residues within 4Å: Chain D: D.303, Q.307, T.308 No protein-ligand interaction detected (PLIP) FMT.30: 2 residues within 4Å: Chain D: Q.229, Q.233 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.233 Water bridges: D:Q.229, D:Q.229 FMT.31: 3 residues within 4Å: Chain D: H.312, S.313, D.319 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.155, D:S.313, D:S.313 Water bridges: D:R.280 FMT.32: 4 residues within 4Å: Chain D: A.44, K.47, E.48, R.114 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.47, D:E.48, D:E.48 Water bridges: D:A.44 FMT.33: 4 residues within 4Å: Chain D: R.164, A.168, E.169, V.170 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.164, D:R.164, D:V.170

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

MLI.3: 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:G.239, A:S.240, A:S.240 Water bridges: A:A.241 MLI.17: 1 residues within 4Å: Chain B: R.236 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.236 MLI.24: 8 residues within 4Å: Chain C: Y.181, G.217, L.218, G.219, I.237, V.238, G.239, S.240 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.181, C:L.218, C:G.219, C:V.220, C:I.237, C:G.239, C:S.240

2 x PZJ: (3R,4R)-4-[4-(2-Chlorophenyl)piperazin-1-yl]-1,1-dioxothiolan-3-ol(Non-covalent)

PZJ.4: 20 residues within 4Å: Chain A: D.64, G.66, M.67, Y.108, D.136 Chain B: Y.29, V.30, P.31, L.34, I.184, F.188, W.191, Y.200, F.202, G.207, P.208, F.211, F.293, H.294, G.295 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.200, B:Y.200, B:F.202, B:F.211, B:F.211 Hydrogen bonds: B:H.294, B:G.295 pi-Stacking: B:F.202 pi-Cation interactions: B:F.188 PZJ.26: 18 residues within 4Å: Chain C: D.64, G.66, M.67, Y.108, D.136 Chain D: Y.29, V.30, P.31, L.34, F.188, W.191, Y.200, F.202, G.207, P.208, F.211, H.294, G.295 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.200, D:Y.200, D:F.202, D:F.211, D:F.211 Hydrogen bonds: D:H.294, D:G.295 pi-Stacking: D:F.202 pi-Cation interactions: D:F.188

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

P1T.5: 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 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.180, 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.27: 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 23 PLIP interactions: 23 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:G.246, D:G.247, D:G.248, D:S.249, D:N.250, D:N.250, D:S.390 Water bridges: D:T.204, D:T.204, D:G.248, D:A.251 Salt bridges: D:H.100, D:K.101, D:K.101 pi-Stacking: D:H.100

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

ACT.9: 3 residues within 4Å: Chain B: E.378, L.379, G.380 No protein-ligand interaction detected (PLIP)

6 x K: POTASSIUM ION(Non-covalent)

K.13: 6 residues within 4Å: Chain B: V.245, G.246, A.282, T.284, Y.320, G.322 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.284, B:Y.320, H2O.7 K.14: 5 residues within 4Å: Chain B: S.177, T.179, S.311, H.312, D.319 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.311, H2O.9 K.15: 1 residues within 4Å: Chain B: D.59 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, H2O.9, H2O.9 K.16: 4 residues within 4Å: Chain B: T.175, N.185, E.186, R.189 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 K.23: 5 residues within 4Å: Chain C: Y.30, V.60, D.68, T.76, Y.108 No protein-ligand interaction detected (PLIP) K.34: 4 residues within 4Å: Chain D: L.237, P.238, D.239, G.263 No protein-ligand interaction detected (PLIP)

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

EDO.18: 3 residues within 4Å: Chain B: R.155, T.399 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.399 EDO.19: 5 residues within 4Å: Chain B: H.18, G.21, P.22, G.24 Ligands: FMT.7 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain B: D.57, R.60, L.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.57, B:R.60, B:R.60 EDO.21: 10 residues within 4Å: Chain B: R.155, Q.156, I.314, S.315, A.316, I.363, E.364, K.395, D.396 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.155, B:Q.156, B:A.316, B:E.364, B:K.395 EDO.25: 4 residues within 4Å: Chain C: M.67, M.106, L.159, A.183 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.35: 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 Hydrogen bonds: D:Y.29, C:Q.144 Water bridges: D:Y.29

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

NA.36: 5 residues within 4Å: Chain D: G.246, A.282, T.284, Y.320, G.322 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.282, D:T.284 NA.37: 4 residues within 4Å: Chain B: P.71 Chain D: A.63, G.67, R.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.68

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

2020-09-30

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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