SMTL ID : 3e08.1 (1 other biounit)

H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 13 residues within 4Å: Chain A: F.51, S.55, Y.113, R.117, L.120, S.123, S.124, G.253, T.254 Chain B: Y.24, Y.27, L.28 Ligands: HEM.2 15 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: A:F.51, A:F.51, A:T.254, B:Y.24, B:Y.24, B:Y.27, B:L.28 Hydrogen bonds: A:S.124, A:T.254, W.1, W.1 Water bridges: A:S.55, A:G.125, W.1 Salt bridges: A:R.117 TRP.3: 9 residues within 4Å: Chain A: R.85, K.92, Y.220, S.221, E.224, D.225, D.228 Chain C: K.86, A.89 15 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C, 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.220, A:E.224, A:E.224, C:K.86 Hydrogen bonds: A:R.85, A:D.225, A:D.225, A:D.228, W.3 Water bridges: A:R.85, A:R.85, C:R.85, D:R.246, D:R.246 Salt bridges: A:K.92 TRP.5: 13 residues within 4Å: Chain A: Y.24, Y.27, L.28 Chain B: F.51, S.55, Y.113, R.117, L.120, S.123, S.124, G.253, T.254 Ligands: HEM.4 14 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.24, A:Y.24, A:Y.27, A:L.28, B:F.51, B:F.51 Hydrogen bonds: B:S.55, B:S.55, B:S.124, B:T.254, W.5, W.5 Salt bridges: B:R.117 Water bridges: W.5 TRP.6: 9 residues within 4Å: Chain B: R.85, K.92, Y.220, S.221, E.224, D.225, D.228 Chain D: K.86, A.89 15 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 interactions with chain C Hydrophobic interactions: B:Y.220, B:E.224, B:E.224, D:K.86, D:K.86 Hydrogen bonds: B:R.85, B:D.225, B:D.225, B:D.228, W.6 Water bridges: B:R.85, B:R.85, C:R.246, C:R.246 Salt bridges: B:K.92 TRP.7: 9 residues within 4Å: Chain A: K.86, A.89 Chain C: R.85, K.92, Y.220, S.221, E.224, D.225, D.228 17 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B, 1 Ligand-Ligand interactions, 3 interactions with chain A Hydrophobic interactions: C:Y.220, C:Y.220, C:E.224, C:E.224, A:K.86, A:K.86 Hydrogen bonds: C:R.85, C:D.225, C:D.228, W.7 Water bridges: C:R.85, C:K.92, C:K.92, B:R.246, B:R.246, A:K.86 Salt bridges: C:K.92 TRP.8: 14 residues within 4Å: Chain C: F.51, S.55, Y.113, R.117, L.120, S.123, S.124, I.248, G.253, T.254 Chain D: Y.24, Y.27, L.28 Ligands: HEM.9 15 PLIP interactions: 9 interactions with chain C, 2 Ligand-Ligand interactions, 4 interactions with chain D Hydrophobic interactions: C:F.51, C:F.51, D:Y.24, D:Y.24, D:Y.27, D:L.28 Hydrogen bonds: C:Y.113, C:S.124, C:T.254, W.8, W.8 Water bridges: C:S.55, C:G.125, C:G.125 Salt bridges: C:R.117 TRP.10: 9 residues within 4Å: Chain B: K.86, A.89 Chain D: R.85, K.92, Y.220, S.221, E.224, D.225, D.228 15 PLIP interactions: 9 interactions with chain D, 3 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrophobic interactions: D:Y.220, D:E.224, D:E.224, B:K.86, B:K.86 Hydrogen bonds: D:R.85, D:D.225, D:D.228, W.10 Water bridges: D:R.85, D:K.92, B:K.86, A:R.246, A:R.246 Salt bridges: D:K.92 TRP.11: 14 residues within 4Å: Chain C: Y.24, Y.27, L.28 Chain D: F.51, S.55, Y.113, R.117, L.120, S.123, S.124, I.248, G.253, T.254 Ligands: HEM.12 14 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: W.11, W.11, D:Y.113, D:S.124, D:T.254 Hydrophobic interactions: D:F.51, C:Y.24, C:Y.24, C:Y.27, C:L.28 Water bridges: D:S.55, D:G.125, D:G.125 Salt bridges: D:R.117

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 27 residues within 4Å: Chain A: F.51, Q.54, S.55, S.58, W.102, L.105, Y.113, S.124, G.125, F.126, Y.131, R.132, W.236, H.240, V.244, V.247, I.248, G.253, T.254, G.255, G.256, S.257, G.259, L.263, A.266 Chain B: R.8 Ligands: TRP.1 25 PLIP interactions: 21 interactions with chain A, 2 Ligand-Ligand interactions, 1 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:F.51, A:Q.54, A:W.102, A:L.105, A:F.126, A:Y.131, A:W.236, A:V.247, A:I.248, A:I.248 Hydrogen bonds: A:S.124, A:G.253, A:T.254, A:G.255, A:G.256, A:S.257, A:S.257, W.1 Water bridges: A:Y.131, A:Y.131, A:Y.131 Salt bridges: A:R.132, B:R.8 pi-Stacking: W.1 Metal complexes: H2O.1 HEM.4: 28 residues within 4Å: Chain A: R.8, Y.24 Chain B: F.51, Q.54, S.55, S.58, W.102, L.105, Y.113, S.124, G.125, F.126, Y.131, R.132, W.236, H.240, V.244, V.247, I.248, G.253, T.254, G.255, G.256, S.257, G.259, L.263, A.266 Ligands: TRP.5 27 PLIP interactions: 23 interactions with chain B, 2 Ligand-Ligand interactions, 1 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: B:F.51, B:Q.54, B:W.102, B:F.126, B:Y.131, B:Y.131, B:W.236, B:V.244, B:V.247, B:I.248, B:L.263 Hydrogen bonds: B:S.124, B:G.253, B:T.254, B:G.255, B:G.256, B:S.257, B:S.257, W.5 Water bridges: B:Y.131, B:Y.131, B:Y.131, B:L.263 Salt bridges: B:R.132, A:R.8 pi-Stacking: W.5 Metal complexes: H2O.13 HEM.9: 27 residues within 4Å: Chain C: F.51, Q.54, S.55, S.58, W.102, L.105, S.124, G.125, F.126, Y.131, R.132, W.236, H.240, V.244, V.247, I.248, G.253, T.254, G.255, G.256, S.257, G.259, L.263, A.266 Chain D: R.8, Y.24 Ligands: TRP.8 24 PLIP interactions: 20 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: C:F.51, C:Q.54, C:W.102, C:W.102, C:F.126, C:Y.131, C:W.236, C:V.247, C:I.248, C:I.248 Hydrogen bonds: C:S.124, C:G.253, C:G.255, C:S.257, C:S.257, W.8 Water bridges: C:R.132, C:R.237, C:L.263 Salt bridges: C:R.132, D:R.8 pi-Stacking: C:W.102, W.8 Metal complexes: H2O.26 HEM.12: 26 residues within 4Å: Chain C: R.8, Y.24 Chain D: Q.54, S.55, S.58, W.102, L.105, S.124, G.125, F.126, Y.131, R.132, W.236, H.240, V.244, V.247, I.248, G.253, T.254, G.255, G.256, S.257, G.259, L.263, A.266 Ligands: TRP.11 25 PLIP interactions: 2 Ligand-Ligand interactions, 21 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Hydrogen bonds: W.11, D:S.124, D:G.253, D:T.254, D:G.255, D:G.256, D:S.257, D:S.257 pi-Stacking: W.11 Hydrophobic interactions: D:Q.54, D:W.102, D:L.105, D:F.126, D:Y.131, D:W.236, D:V.247, D:I.248, D:I.248, D:L.263 Water bridges: D:R.132, D:R.132, D:E.135 Salt bridges: D:R.132, C:R.8 Metal complexes: H2O.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thackray, S.J. et al., Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding. Biochemistry (2008)

Release Date

2008-09-30

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophan 2,3-dioxygenase

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