SMTL ID : 9bnj.1

Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: G.53, N.271 Chain B: E.70, A.305, G.306 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.70, A:G.53, A:N.271, H2O.8, H2O.22 K.6: 6 residues within 4Å: Chain A: E.70, A.305, G.306 Chain B: G.53, K.265, N.271 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.53, B:N.271, A:E.70, H2O.6, H2O.22 K.10: 6 residues within 4Å: Chain C: G.53, K.265, N.271 Chain D: E.70, A.305, G.306 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:G.53, C:N.271, D:E.70, H2O.40, H2O.57 K.13: 6 residues within 4Å: Chain C: E.70, A.305, G.306 Chain D: G.53, K.265, N.271 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:G.53, D:N.271, C:E.70, H2O.41, H2O.56

5 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.2: 14 residues within 4Å: Chain A: F.37, L.49, T.50, R.101, F.132, D.133, T.134, V.389, I.391, L.395, R.414, F.459 Chain B: Y.72 Ligands: 0JO.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.37, A:F.37, A:F.132, A:V.389, A:L.395, A:F.459, B:Y.72 Hydrogen bonds: A:R.101, A:D.133 Water bridges: A:R.101 pi-Stacking: A:F.459 BZI.5: 3 residues within 4Å: Chain A: Y.160, R.340, Y.348 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.160, A:Y.160, A:Y.348 Hydrogen bonds: A:Y.348 Water bridges: A:R.340 pi-Stacking: A:Y.160 BZI.8: 15 residues within 4Å: Chain A: Y.72 Chain B: F.37, L.49, T.50, R.101, F.132, D.133, T.134, V.389, I.391, L.395, R.414, H.458, F.459 Ligands: 0JO.9 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.72, B:F.37, B:V.389 Hydrogen bonds: A:Y.72, B:D.133, B:D.133 Water bridges: B:R.101 pi-Stacking: B:F.459 BZI.11: 15 residues within 4Å: Chain C: F.37, L.49, T.50, R.101, F.132, D.133, T.134, V.389, I.391, L.395, R.414, H.458, F.459 Chain D: Y.72 Ligands: 0JO.12 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.37, C:F.132, C:V.389 Hydrogen bonds: C:D.133 Water bridges: C:R.101 pi-Stacking: C:F.459 BZI.14: 15 residues within 4Å: Chain C: Y.72 Chain D: F.37, L.49, T.50, R.101, F.132, D.133, T.134, V.389, I.391, L.395, R.414, H.458, F.459 Ligands: 0JO.15 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.37, D:V.389, C:Y.72 Hydrogen bonds: D:R.101, D:D.133 pi-Stacking: D:F.459

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: Y.232, F.233, A.236, R.237, I.329, K.333, P.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.237, A:R.237

4 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.4: 20 residues within 4Å: Chain A: T.50, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, A.225, R.226, S.263, K.265, K.266, R.414 Chain B: Y.72 Ligands: BZI.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.132, A:F.132, A:T.190 Hydrogen bonds: A:T.50, A:Q.99, A:G.100, A:R.101, A:N.194, A:R.226, A:R.226, A:S.263, A:K.266 Water bridges: A:S.52, A:A.225 Salt bridges: A:R.101, A:R.226, A:K.265, A:K.266, A:K.266, A:R.414 0JO.9: 20 residues within 4Å: Chain A: Y.72 Chain B: T.50, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, A.225, R.226, S.263, K.265, K.266, R.414 Ligands: BZI.8 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.132, B:F.132, B:F.132, B:T.190 Hydrogen bonds: B:T.50, B:S.52, B:S.52, B:Q.99, B:G.100, B:R.101, B:N.194, B:R.226, B:R.226, B:S.263, B:K.266 Water bridges: B:A.225, B:K.265 Salt bridges: B:R.101, B:R.226, B:K.265, B:K.266, B:K.266, B:R.414 0JO.12: 20 residues within 4Å: Chain C: T.50, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, A.225, R.226, S.263, K.265, K.266, R.414 Chain D: Y.72 Ligands: BZI.11 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:F.132, C:F.132, C:T.190 Hydrogen bonds: C:T.50, C:S.52, C:Q.99, C:G.100, C:R.101, C:N.194, C:R.226, C:R.226, C:S.263, C:K.266 Water bridges: C:A.225, C:K.265 Salt bridges: C:R.101, C:R.226, C:K.265, C:K.266, C:K.266, C:R.414 0JO.15: 20 residues within 4Å: Chain C: Y.72 Chain D: T.50, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, A.225, R.226, S.263, K.265, K.266, R.414 Ligands: BZI.14 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:F.132, D:F.132, D:T.190 Hydrogen bonds: D:T.50, D:T.50, D:S.52, D:Q.99, D:G.100, D:R.101, D:N.194, D:R.226, D:R.226, D:S.263, D:K.266 Water bridges: D:S.52, D:A.225 Salt bridges: D:R.101, D:R.226, D:K.265, D:K.266, D:K.266, D:R.414

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain B: N.123, V.125, H.179, N.183 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S., Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole. To Be Published

Release Date

2024-05-29

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophanase

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