SMTL ID : 6usa.1 (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

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

FMT.1: 4 residues within 4Å: Chain A: G.69, P.70, T.71, S.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.71, A:T.71, A:S.240 Water bridges: A:I.72 FMT.2: 7 residues within 4Å: Chain A: Y.30, E.57, I.72, M.106, Y.181, I.237 Ligands: MLI.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.57 FMT.6: 3 residues within 4Å: Chain B: G.351, R.355 Chain D: L.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.355, B:R.355 FMT.7: 4 residues within 4Å: Chain B: A.44, K.47, E.48, R.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.47 FMT.8: 3 residues within 4Å: Chain B: V.160, R.164, V.170 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.164, B:V.170 Water bridges: B:V.170 FMT.9: 8 residues within 4Å: Chain B: N.95, H.96, T.97, G.98, R.392 Chain D: D.93, L.94, R.392 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.96, B:T.97, B:R.392, B:R.392, D:D.93 FMT.10: 3 residues within 4Å: Chain B: L.165 Chain D: G.351, R.355 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:L.165, D:R.355 FMT.15: 4 residues within 4Å: Chain C: R.122, A.125, A.126, H.152 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.126, C:H.152 FMT.19: 2 residues within 4Å: Chain C: Q.144 Chain D: F.297 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.24 FMT.20: 4 residues within 4Å: Chain D: H.11, L.259, D.260, R.335 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.11, D:D.260 FMT.22: 3 residues within 4Å: Chain D: R.164, E.169, V.170 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.169, D:V.170 FMT.23: 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.24: 5 residues within 4Å: Chain D: H.11, R.220, H.256, A.257, D.260 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.220, D:D.260 Water bridges: D:D.260

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

MLI.3: 8 residues within 4Å: Chain A: Y.181, G.217, L.218, G.219, 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:V.220, A:V.220, A:S.240 MLI.16: 8 residues within 4Å: Chain C: Y.181, G.217, L.218, G.219, I.237, V.238, G.239, S.240 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.181, C:G.219, C:I.237, C:G.239, C:S.240 Water bridges: C:S.240 MLI.29: 1 residues within 4Å: Chain D: R.236 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.236

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

PZJ.4: 19 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, 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:W.191, B:Y.200, B:F.202, B:P.208, B:F.211, B:F.211 Hydrogen bonds: B:H.294, B:G.295 pi-Stacking: B:F.202 PZJ.17: 20 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, I.184, F.188, W.191, Y.200, F.202, G.207, P.208, F.211, F.293, H.294, G.295 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: 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 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:N.250, B:N.250, B:S.390 Water bridges: B:E.123, B:G.248, B:A.251 Salt bridges: B:H.100, B:K.101, B:K.101 pi-Stacking: B:H.100 P1T.18: 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 25 PLIP interactions: 25 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.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

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.11: 6 residues within 4Å: Chain B: V.245, G.246, A.282, T.284, Y.320, G.322 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.320, H2O.7 K.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.27: 6 residues within 4Å: Chain D: V.245, G.246, A.282, T.284, Y.320, G.322 No protein-ligand interaction detected (PLIP) K.28: 1 residues within 4Å: Chain D: Q.231 No protein-ligand interaction detected (PLIP)

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

EDO.12: 6 residues within 4Å: Chain B: V.171, A.172, V.173, Q.174, T.175, E.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.174, B:T.175 EDO.13: 4 residues within 4Å: Chain B: H.11, L.259, A.333, R.335 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.11, B:L.259 EDO.30: 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.31: 1 residues within 4Å: Chain D: W.403 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.403

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

PEG.14: 7 residues within 4Å: Chain C: Y.62, S.63, P.65, A.73, T.76, E.77, L.80 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.76

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

ACT.21: 4 residues within 4Å: Chain D: P.262, G.263, V.264, R.265 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.264 Salt bridges: D:R.265 ACT.25: 2 residues within 4Å: Chain D: E.378, L.379 No protein-ligand interaction detected (PLIP)

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
A

C
C

B
B

D
D

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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