SMTL ID : 3bk9.2 (1 other biounit)

H55A mutant of tryptophan 2,3-dioxygenase from Xanthomonas campestris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

5 x TRP: TRYPTOPHAN(Non-covalent)

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

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

HEM.2: 26 residues within 4Å: Chain A: F.51, Q.54, A.55, S.58, W.102, L.105, L.108, S.124, G.125, F.126, Y.131, R.132, W.236, H.240, V.244, I.248, G.253, T.254, G.255, G.256, S.257, G.259, L.263, A.266 Chain B: Y.24 Ligands: TRP.1 20 PLIP interactions: 18 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: A:F.51, A:Q.54, A:W.102, A:W.102, A:L.108, A:F.126, A:Y.131, A:W.236, A:I.248, A:I.248, A:L.263 Hydrogen bonds: A:S.124, A:G.255, A:S.257, A:S.257 Salt bridges: A:R.132 pi-Stacking: A:W.102, W.1 Metal complexes: A:H.240, H2O.1 HEM.5: 26 residues within 4Å: Chain A: Y.24 Chain B: F.51, Q.54, S.58, W.102, L.105, L.108, 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.4 28 PLIP interactions: 25 interactions with chain B, 2 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: B:F.51, B:Q.54, B:W.102, B:W.102, B:L.105, B:L.108, B:Y.131, B:Y.131, B:W.236, B:V.244, B:V.247, B:I.248, B:L.263, B:L.263 Hydrogen bonds: B:S.124, B:T.254, B:G.255, B:G.256, B:S.257, B:S.257 Water bridges: B:R.132, B:R.132 Salt bridges: B:R.132 pi-Stacking: B:W.102, W.4, W.4 Metal complexes: B:H.240, H2O.6 HEM.7: 26 residues within 4Å: Chain C: F.51, Q.54, 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, F.262, L.263, A.266 Chain D: Y.24 Ligands: TRP.6 22 PLIP interactions: 20 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: C:F.51, C:Q.54, C:L.105, C:Y.131, C:W.236, C:V.247, C:I.248, C:I.248, C:F.262, C:L.263 Hydrogen bonds: C:S.124, C:G.255, C:G.256, C:S.257, C:S.257 Water bridges: C:R.132, C:R.132 Salt bridges: C:R.132 pi-Stacking: C:W.102, W.6 Metal complexes: C:H.240, H2O.10 HEM.9: 24 residues within 4Å: Chain C: Y.24 Chain D: F.51, Q.54, A.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, G.253, T.254, G.255, G.256, S.257, G.259, A.266 Ligands: TRP.8 20 PLIP interactions: 17 interactions with chain D, 2 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: D:F.51, D:Q.54, D:W.102, D:F.126, D:Y.131, D:Y.131, D:W.236, D:V.247 Hydrogen bonds: D:S.124, D:G.253, D:T.254, D:G.255, D:G.256, D:S.257, D:S.257 Salt bridges: D:R.132 Metal complexes: D:H.240, H2O.17 pi-Stacking: W.8, W.8

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
E

B
F

C
G

D
H

Tryptophan 2,3-dioxygenase

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