SMTL ID : 7p46.1 (1 other biounit)

Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 29 residues within 4Å: Chain A: F.47, Q.50, S.51, S.54, W.98, L.101, Y.109, S.120, G.121, F.122, Y.127, R.128, W.232, H.236, V.240, V.243, I.244, G.249, T.250, G.251, G.252, S.253, G.255, L.259, A.262 Chain B: R.4, Y.20 Ligands: CYN.2, KYN.3 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.47, A:Q.50, A:W.98, A:F.122, A:Y.127, A:W.232, A:V.243, A:I.244 Hydrogen bonds: A:S.120, A:T.250, A:G.251, A:G.252, A:S.253, A:S.253 Water bridges: A:Y.127, A:Y.127, A:E.131, B:R.4 Salt bridges: A:R.128, B:R.4 Metal complexes: A:H.236 HEM.11: 28 residues within 4Å: Chain A: R.4, Y.20 Chain B: F.47, Q.50, S.51, S.54, W.98, L.101, S.120, G.121, F.122, Y.127, R.128, W.232, H.236, V.240, V.243, I.244, G.249, T.250, G.251, G.252, S.253, G.255, L.259, A.262 Ligands: CYN.12, KYN.13 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:F.47, B:Q.50, B:W.98, B:F.122, B:Y.127, B:V.243, B:I.244 Hydrogen bonds: B:S.120, B:S.120, B:T.250, B:G.251, B:G.252, B:S.253 Water bridges: B:Y.127, B:R.128, B:R.128 Salt bridges: B:R.128, A:R.4 Metal complexes: B:H.236 HEM.17: 28 residues within 4Å: Chain C: F.47, Q.50, S.51, S.54, W.98, L.101, S.120, G.121, F.122, Y.127, R.128, W.232, H.236, V.240, V.243, I.244, G.249, T.250, G.251, G.252, S.253, G.255, L.259, A.262 Chain D: R.4, Y.20 Ligands: CYN.18, KYN.19 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:F.47, C:Q.50, C:W.98, C:F.122, C:Y.127, C:V.243, C:I.244, C:I.244 Hydrogen bonds: C:S.120, C:S.120, C:G.251, C:G.252, C:S.253 Water bridges: C:R.128, C:R.128, C:L.259 Salt bridges: C:R.128, D:R.4 Metal complexes: C:H.236 HEM.23: 28 residues within 4Å: Chain C: R.4, Y.20 Chain D: F.47, Q.50, S.51, S.54, W.98, L.101, S.120, G.121, F.122, Y.127, R.128, W.232, H.236, V.240, V.243, I.244, G.249, T.250, G.251, G.252, S.253, G.255, L.259, A.262 Ligands: CYN.24, KYN.25 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:F.47, D:Q.50, D:W.98, D:F.122, D:Y.127, D:V.243, D:I.244, D:I.244 Hydrogen bonds: D:S.120, D:G.249, D:T.250, D:G.251, D:G.252, D:S.253, D:S.253 Water bridges: D:R.128, D:R.128, D:E.131, D:L.259 Salt bridges: D:R.128, C:R.4 pi-Stacking: D:H.236 Metal complexes: D:H.236

4 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 5 residues within 4Å: Chain A: S.120, G.121, H.236 Ligands: HEM.1, KYN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.121 CYN.12: 5 residues within 4Å: Chain B: S.120, G.121, H.236 Ligands: HEM.11, KYN.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.121 CYN.18: 4 residues within 4Å: Chain C: S.120, G.121 Ligands: HEM.17, KYN.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.120, C:G.121 CYN.24: 4 residues within 4Å: Chain D: S.120, G.121 Ligands: HEM.23, KYN.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.121

4 x KYN: (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid(Non-covalent)

KYN.3: 13 residues within 4Å: Chain A: F.47, S.51, Y.109, R.113, L.116, S.119, S.120, G.249, T.250 Chain B: Y.20, Y.23 Ligands: HEM.1, CYN.2 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.20, B:Y.20, B:Y.23, A:F.47, A:F.47, A:L.116 Hydrogen bonds: A:S.51, A:S.51, A:Y.109, A:S.120, A:T.250 Salt bridges: A:R.113 KYN.13: 14 residues within 4Å: Chain A: Y.20, Y.23 Chain B: F.47, S.51, Y.109, R.113, L.116, S.119, S.120, I.244, G.249, T.250 Ligands: HEM.11, CYN.12 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.47, B:L.116, A:Y.20, A:Y.20, A:Y.23 Hydrogen bonds: B:S.51, B:S.51, B:Y.109, B:S.120, B:T.250 Salt bridges: B:R.113 KYN.19: 14 residues within 4Å: Chain C: F.47, S.51, Y.109, R.113, S.119, S.120, I.244, G.249, T.250 Chain D: Y.20, Y.23, L.24 Ligands: HEM.17, CYN.18 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.47, C:F.47, D:Y.20, D:Y.20, D:Y.23, D:L.24 Hydrogen bonds: C:S.51, C:S.51, C:Y.109, C:Y.109, C:S.120, C:T.250 Salt bridges: C:R.113 KYN.25: 14 residues within 4Å: Chain C: Y.20, Y.23 Chain D: F.47, S.51, Y.109, R.113, L.116, S.119, S.120, I.244, G.249, T.250 Ligands: HEM.23, CYN.24 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.47, D:F.47, D:L.116, C:Y.20, C:Y.20, C:Y.23 Hydrogen bonds: D:S.51, D:S.51, D:Y.109, D:Y.109, D:S.120, D:T.250 Salt bridges: D:R.113

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.4: 9 residues within 4Å: Chain A: R.81, K.88, Y.216, S.217, E.220, D.221, D.224 Chain D: K.82, A.85 15 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C, 10 interactions with chain A, Hydrophobic interactions: D:K.82, D:K.82, A:Y.216, A:Y.216, A:E.220, A:E.220 Water bridges: D:R.81, C:R.242, C:R.242, A:R.81, A:R.81 Hydrogen bonds: A:R.81, A:D.221, A:D.224 Salt bridges: A:K.88 TRP.14: 9 residues within 4Å: Chain B: R.81, K.88, Y.216, S.217, E.220, D.221, D.224 Chain C: K.82, A.85 16 PLIP interactions: 2 interactions with chain D, 9 interactions with chain B, 5 interactions with chain C Water bridges: D:R.242, D:R.242, B:R.81, C:K.82, C:A.85, C:Q.89 Hydrophobic interactions: B:Y.216, B:Y.216, B:E.220, B:E.220, C:K.82, C:K.82 Hydrogen bonds: B:R.81, B:D.221, B:D.224 Salt bridges: B:K.88 TRP.20: 9 residues within 4Å: Chain B: K.82, A.85 Chain C: R.81, K.88, Y.216, S.217, E.220, D.221, D.224 16 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A, 12 interactions with chain C, 1 interactions with chain B Hydrogen bonds: W.20, C:R.81, C:D.221, C:D.224 Water bridges: A:R.242, A:R.242, C:R.81, C:R.81, C:K.88, C:K.88 Hydrophobic interactions: C:Y.216, C:Y.216, C:E.220, C:E.220, B:K.82 Salt bridges: C:K.88 TRP.26: 9 residues within 4Å: Chain A: K.82, A.85 Chain D: R.81, K.88, Y.216, S.217, E.220, D.221, D.224 17 PLIP interactions: 11 interactions with chain D, 4 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: D:Y.216, D:Y.216, D:E.220, D:E.220, A:K.82, A:K.82 Hydrogen bonds: D:R.81, D:D.221, D:D.224, W.26 Water bridges: D:R.81, D:K.88, D:K.88, A:R.81, A:K.82, B:R.242 Salt bridges: D:K.88

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: F.234, M.237, Q.260, L.263 Chain C: L.263 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:L.263, C:L.263 Hydrogen bonds: A:Q.260 GOL.6: 4 residues within 4Å: Chain A: R.25, L.26, D.27, Q.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:D.27, A:Q.28 Water bridges: A:L.26 GOL.7: 7 residues within 4Å: Chain A: K.59, A.62, R.66, L.125, Q.126, Y.129, R.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.66, A:R.66, A:Q.126 Water bridges: A:H.63, A:Y.129 GOL.8: 6 residues within 4Å: Chain A: S.99, E.102, R.235 Chain B: Q.89 Chain C: D.224, Q.228 8 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Water bridges: B:Q.89, B:Q.89, A:R.242, C:K.88, C:Q.228 Hydrogen bonds: A:E.102, A:R.235, C:D.224 GOL.9: 4 residues within 4Å: Chain A: A.67, H.71, V.83 Chain B: H.42 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.108, B:E.108, A:H.71 Water bridges: B:H.42 GOL.10: 3 residues within 4Å: Chain A: E.203, E.207, S.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.203, A:E.203, A:E.207 Water bridges: A:G.279 GOL.15: 5 residues within 4Å: Chain A: D.148, A.150, G.151 Chain B: D.27 Ligands: GOL.16 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.27, A:A.150 Hydrogen bonds: A:G.151 GOL.16: 5 residues within 4Å: Chain A: D.148 Chain B: T.19, G.21, G.22 Ligands: GOL.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.19, B:G.22, A:D.148 Water bridges: B:G.21, B:L.26, A:D.148 GOL.21: 4 residues within 4Å: Chain C: H.11, T.12, D.13, R.17 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.11, C:T.12, C:T.12, C:D.13, C:R.17 GOL.22: 6 residues within 4Å: Chain C: A.62, R.66, L.125, Q.126, Y.129, R.154 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.66, C:R.66, C:R.154, C:R.154 Water bridges: C:Q.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basran, J. et al., Binding of l-kynurenine to X. campestris tryptophan 2,3-dioxygenase. J.Inorg.Biochem. (2021)

Release Date

2021-10-06

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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