SMTL ID : 5ti9.1

Crystal structure of human TDO in complex with Trp and dioxygen, Northeast Structural Genomics Consortium Target HR6161

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.1: 5 residues within 4Å: Chain A: H.60, S.135, G.136 Ligands: HEM.2, TRP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.136, W.3, W.3 OXY.6: 4 residues within 4Å: Chain B: S.135, G.136 Ligands: HEM.7, TRP.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.136, W.8

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

HEM.2: 31 residues within 4Å: Chain A: F.56, H.60, Y.63, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, N.160, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain B: Y.26 Ligands: OXY.1, TRP.3 28 PLIP interactions: 26 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.56, A:Y.63, A:Y.63, A:Y.63, A:F.124, A:F.124, A:F.137, A:F.142, A:W.308, A:M.319, A:L.320, A:L.320, A:L.335 Hydrogen bonds: A:S.135, A:S.135, A:R.309, A:T.326, A:G.327, A:G.328, A:S.329, A:Y.334, W.3 Water bridges: A:R.143, A:N.160 Salt bridges: A:R.143 pi-Cation interactions: A:H.60 Metal complexes: A:H.312 pi-Stacking: W.3 HEM.7: 32 residues within 4Å: Chain A: Y.26 Chain B: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Ligands: OXY.6, TRP.8 31 PLIP interactions: 27 interactions with chain B, 4 Ligand-Ligand interactions Hydrophobic interactions: B:F.56, B:T.59, B:Y.63, B:Y.63, B:Y.63, B:F.67, B:F.124, B:F.137, B:F.137, B:F.142, B:W.308, B:L.320, B:L.335, B:L.335 Hydrogen bonds: B:S.135, B:S.135, B:R.309, B:G.327, B:G.328, B:S.329, B:Y.334, W.8, W.8 Water bridges: B:R.143, B:R.156, B:T.338 Salt bridges: B:R.143 pi-Cation interactions: B:H.60 Metal complexes: B:H.312 pi-Stacking: W.8, W.8 HEM.11: 31 residues within 4Å: Chain C: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain D: Y.26 Ligands: NFK.12 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:F.56, C:T.59, C:Y.63, C:Y.63, C:Y.63, C:F.67, C:F.124, C:F.137, C:F.142, C:W.308, C:M.319, C:L.320, C:L.335 Hydrogen bonds: C:S.135, C:R.309, C:G.327, C:G.328, C:S.329, C:S.329, C:Y.334, C:T.338 Salt bridges: C:R.143 pi-Stacking: C:H.60 Metal complexes: C:H.312 HEM.14: 25 residues within 4Å: Chain C: Y.26 Chain D: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, S.135, G.136, F.137, F.142, R.143, Y.159, W.308, R.309, H.312, M.315, V.316, M.319, L.320, Y.334, L.335, T.338 Ligands: NFK.15 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:F.56, D:T.59, D:Y.63, D:Y.63, D:Y.63, D:F.67, D:F.137, D:F.142, D:W.308, D:M.319, D:L.320, D:L.335, D:L.335 Hydrogen bonds: D:S.135, D:S.135, D:R.309 Water bridges: D:T.338 Salt bridges: D:R.143 pi-Stacking: D:H.60 Metal complexes: D:H.312

6 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 14 residues within 4Å: Chain A: F.56, H.60, F.124, R.128, L.131, A.134, S.135, L.320, G.325, T.326 Chain B: Y.26, Y.29 Ligands: OXY.1, HEM.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.56, A:L.131, A:A.134, A:T.326, B:Y.26, B:Y.26, B:Y.29 Hydrogen bonds: A:H.60, A:S.135, A:T.326 Salt bridges: A:R.128 pi-Stacking: A:F.56, A:H.60 TRP.4: 10 residues within 4Å: Chain A: V.86, R.87, E.89, W.192, R.195, T.196, P.197, R.287, F.288, P.291 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.192, A:P.197, A:F.288, A:P.291 Hydrogen bonds: A:E.89, A:E.89, A:W.192, W.4, W.4 Salt bridges: A:R.87, A:R.195 TRP.8: 14 residues within 4Å: Chain A: Y.26, Y.29 Chain B: F.56, H.60, F.124, R.128, L.131, A.134, S.135, L.320, G.325, T.326 Ligands: OXY.6, HEM.7 13 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.26, A:Y.26, A:Y.29, B:F.56, B:L.131, B:L.131, B:A.134 Hydrogen bonds: B:H.60, B:T.326, W.8, W.8 Salt bridges: B:R.128 pi-Stacking: B:F.56 TRP.9: 11 residues within 4Å: Chain B: V.86, R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:W.192, B:T.196, B:P.197, B:I.279, B:F.288, B:P.291 Hydrogen bonds: B:E.89, B:W.192 Salt bridges: B:R.87, B:R.195 TRP.13: 11 residues within 4Å: Chain C: V.86, R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:W.192, C:T.196, C:P.197, C:I.279, C:F.288, C:P.291 Hydrogen bonds: C:E.89, C:E.89, C:W.192 Salt bridges: C:R.87, C:R.195 TRP.16: 11 residues within 4Å: Chain D: V.86, R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 11 PLIP interactions: 1 Ligand-Ligand interactions, 10 interactions with chain D Hydrogen bonds: W.16, D:V.86, D:R.87, D:W.192 Hydrophobic interactions: D:W.192, D:P.197, D:I.279, D:F.288, D:P.291 Salt bridges: D:R.87, D:R.195

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: H.100, V.104, K.107 Chain D: H.100, V.104, K.107 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Salt bridges: D:H.100, D:K.107, A:H.100, A:K.107 PO4.10: 5 residues within 4Å: Chain B: H.100, V.104, K.107 Chain C: H.100, K.107 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Salt bridges: C:H.100, C:K.107, B:H.100, B:K.107 Water bridges: B:K.107, B:K.107

2 x NFK: N'-Formylkynurenine(Non-covalent)

NFK.12: 14 residues within 4Å: Chain C: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, L.320, G.325, T.326 Chain D: Y.26, Y.29 Ligands: HEM.11 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:Y.26, D:Y.29, C:L.131, C:A.134, C:T.326 Hydrogen bonds: C:H.60, C:G.136, C:T.326, C:T.326 Salt bridges: C:R.128 pi-Stacking: C:F.56 NFK.15: 13 residues within 4Å: Chain C: Y.26, Y.29 Chain D: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, H.312, L.320 Ligands: HEM.14 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.131, D:A.134, C:Y.26, C:Y.26, C:Y.29 Hydrogen bonds: D:G.136 Salt bridges: D:R.128 pi-Stacking: D:F.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis-Ballester, A. et al., Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. Sci Rep (2016)

Release Date

2016-10-26

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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