SMTL ID : 8v6p.1

Proteus vulgaris tryptophan indole-lyase complexed with 7-aza-L-tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

2 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.4, H2O.16 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.4, H2O.7

2 x 01: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine

01.3: 24 residues within 4Å: Chain A: 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, L.395, R.414, H.458, F.459 Chain B: Y.72 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.132, A:F.132, A:T.190, A:V.389 Hydrogen bonds: A:D.51, A:S.52, A:Q.99, A:G.100, A:R.101, A:T.135, 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 pi-Stacking: A:F.132 01.6: 20 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, R.226, S.263, K.265, K.266, R.414 Chain D: Y.72 27 PLIP interactions: 26 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.50, C:F.132, C:T.190 Hydrogen bonds: C:D.51, C:S.52, C:Q.99, C:G.100, C:R.101, C:R.101, C:D.133, C:T.135, C:N.194, C:R.226, C:R.226, C:S.263, C:K.266 Water bridges: C:S.52, C:A.225, D:Y.72 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

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

DMS.4: 4 residues within 4Å: Chain A: K.16, S.41, V.44 Chain B: D.69 No protein-ligand interaction detected (PLIP)

2 x 02: (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)propanoic acid

02.5: 25 residues within 4Å: Chain A: Y.72 Chain B: F.37, 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, L.395, R.414, H.458, F.459 28 PLIP interactions: 28 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:D.51, 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:R.101, 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 02.7: 25 residues within 4Å: Chain C: Y.72 Chain D: F.37, 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, L.395, R.414, H.458, F.459 26 PLIP interactions: 2 interactions with chain C, 24 interactions with chain D Water bridges: C:Y.72, C:Y.301, D:A.225 Hydrophobic interactions: D:F.37, D:F.132, D:F.132, D:T.190, D:N.194, D:V.389 Hydrogen bonds: D:T.50, D:S.52, D:Q.99, D:G.100, D:R.101, D:D.133, D:N.194, D:R.226, D:R.226, D:S.263, D:K.266 Salt bridges: D:R.101, D:R.226, D:K.265, D:K.266, D:K.266, D:R.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-01-31

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophanase

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