SMTL ID : 9blv.1

Proteus vulgaris tryptophan indole-lyase complexed with L-Trp and benzimidazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: G.53, N.271 Chain B: E.70 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:G.53, A:N.271, B:E.70, H2O.1, H2O.13 K.2: 3 residues within 4Å: Chain A: E.70 Chain B: G.53, 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.12 K.8: 3 residues within 4Å: Chain C: E.70 Chain D: G.53, 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.20, H2O.23 K.9: 3 residues within 4Å: Chain C: G.53, N.271 Chain D: E.70 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.31, H2O.32

2 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.3: 10 residues within 4Å: Chain A: F.37, R.101, F.132, D.133, V.389, L.395, R.414, F.459 Chain B: Y.72 Ligands: 0JO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.37, A:F.132, A:V.389, A:L.395 Hydrogen bonds: A:R.101, A:D.133 pi-Stacking: A:F.459 BZI.11: 6 residues within 4Å: Chain C: Y.72 Chain D: F.37, R.101, F.132, R.414 Ligands: 0JO.12 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.37, D:F.132, C:Y.72 Hydrogen bonds: D:R.101 Water bridges: D:R.101

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

0JO.4: 18 residues within 4Å: Chain A: T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.266, R.414 Ligands: BZI.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.132, A:F.132, A:T.190 Hydrogen bonds: A:S.52, A:S.52, 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:E.104, A:A.225, A:K.265 Salt bridges: A:R.101, A:R.226, A:K.265, A:K.266, A:K.266, A:R.414 0JO.12: 19 residues within 4Å: Chain D: T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, R.414 Ligands: BZI.11 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.132, D:F.132, D:T.190 Hydrogen bonds: D:T.50, D:S.52, D:S.52, D:Q.99, D:G.100, D:R.101, D:T.135, D:N.194, D:R.226, D:R.226, D:S.263, D:K.266 Water bridges: D:A.225, D:K.265, C:Y.72 Salt bridges: D:R.101, D:R.226, D:K.265, D:K.266, D:K.266, D:R.414 pi-Stacking: D:F.132

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

DMS.5: 1 residues within 4Å: Chain A: K.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.122 DMS.6: 3 residues within 4Å: Chain B: K.333, D.337, Y.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.333 Salt bridges: B:D.337

1 x PLT: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE(Non-covalent)

PLT.7: 23 residues within 4Å: Chain A: Y.72 Chain B: F.37, L.49, T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, T.134, T.135, T.190, N.194, D.223, R.226, S.263, K.265, K.266, V.389, R.414 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:F.37, B:F.132, B:F.132, B:T.190, B:V.389 Hydrogen bonds: B:T.50, B:S.52, B:S.52, B:Q.99, B:G.100, B:R.101, B:D.133, B:T.135, 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 pi-Stacking: B:F.132

1 x 01: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tryptophan

01.10: 21 residues within 4Å: Chain C: T.50, D.51, S.52, Q.99, G.100, R.101, E.104, F.132, D.133, 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 28 PLIP interactions: 1 interactions with chain D, 27 interactions with chain C Water bridges: D:Y.72, C:S.52, C:R.101, C:A.225 Hydrophobic interactions: C:F.132, C:T.190 Hydrogen bonds: C:T.50, C:D.51, C:D.51, C:S.52, C:Q.99, C:G.100, C:R.101, C:R.101, C:N.194, C:R.226, C:R.226, C:S.263, C:K.266, C:K.266 Salt bridges: C:R.101, C:R.226, C:K.265, C:K.266, C:K.266, C:R.414 pi-Stacking: C:F.132, C:F.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism. Acs Catalysis (2024)

Release Date

2025-02-12

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophanase

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