SMTL ID : 8v4a.1

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 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: 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.4, H2O.13 K.3: 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.4, H2O.6 K.6: 3 residues within 4Å: Chain C: G.53, N.271 Chain D: E.70 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.70, C:G.53, H2O.27, H2O.37 K.8: 3 residues within 4Å: Chain C: E.70 Chain D: G.53, N.271 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:G.53, C:E.70, H2O.28, H2O.39, H2O.40

2 x YAE: (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine(Non-covalent)

YAE.2: 21 residues within 4Å: Chain A: F.37, L.49, T.50, 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, F.459 Chain B: Y.72 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.37, A:F.132, A:F.132, A:F.132, A:T.190, B:Y.72 Hydrogen bonds: 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:A.225, A:K.265, B:Y.301 Salt bridges: A:R.101, A:R.226, A:K.265, A:K.266, A:K.266, A:R.414 YAE.7: 19 residues within 4Å: Chain C: F.37, T.50, 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 Chain D: Y.72 24 PLIP interactions: 1 interactions with chain D, 23 interactions with chain C Water bridges: D:Y.301, C:S.52, C:A.225 Hydrophobic interactions: C:F.37, C:F.132, C:T.190 Hydrogen bonds: C:T.50, C:S.52, C:Q.99, C:G.100, C:R.101, C:T.135, C:N.194, C:R.226, C:R.226, C:S.263, 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

2 x YAR: (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid(Non-covalent)

YAR.4: 21 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, R.226, S.263, K.265, K.266, L.395, R.414, H.458, F.459 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.132, B:F.132, B:T.190, B:L.395 Hydrogen bonds: B:T.50, B:T.50, B:S.52, B:Q.99, B:G.100, B:R.101, B:T.135, B:N.194, B:D.223, 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 YAR.9: 21 residues within 4Å: Chain C: Y.72 Chain D: F.37, L.49, T.50, 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, F.459 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:F.37, D:F.132, D:F.132, D:T.190 Hydrogen bonds: D:T.50, D:S.52, D:Q.99, D:G.100, D:R.101, D:N.194, D:D.223, D:R.226, D:R.226, D:S.263, D:K.266 Water bridges: D:A.225, D:K.265, D:K.265 Salt bridges: D:R.101, D:R.226, D:K.265, D:K.266, D:K.266, D:R.414

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

DMS.5: 7 residues within 4Å: Chain B: S.58, H.60, E.318, E.321 Chain D: V.14, E.15, K.16 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:K.16, D:K.16 Hydrogen bonds: B:H.60 Salt bridges: B:E.318, B:E.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S., Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine. To Be Published

Release Date

2023-12-13

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophanase

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