SMTL ID : 1wur.1

Structure of GTP cyclohydrolase I Complexed with 8-oxo-dGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.108, H.111, C.179 Ligands: 8DG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.108, A:H.111, A:C.179 ZN.4: 4 residues within 4Å: Chain B: C.108, H.111, C.179 Ligands: 8DG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.108, B:H.111, B:C.179 ZN.5: 4 residues within 4Å: Chain C: C.108, H.111, C.179 Ligands: 8DG.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.108, C:H.111, C:C.179 ZN.7: 4 residues within 4Å: Chain D: C.108, H.111, C.179 Ligands: 8DG.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.108, D:H.111, D:C.179 ZN.10: 4 residues within 4Å: Chain E: C.108, H.111, C.179 Ligands: 8DG.3 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.108, E:H.111, E:C.179 ZN.11: 4 residues within 4Å: Chain F: C.108, H.111, C.179 Ligands: 8DG.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.108, F:H.111, F:C.179 ZN.14: 4 residues within 4Å: Chain G: C.108, H.111, C.179 Ligands: 8DG.16 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.108, G:H.111, G:C.179 ZN.15: 4 residues within 4Å: Chain H: C.108, H.111, C.179 Ligands: 8DG.18 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.108, H:H.111, H:C.179 ZN.17: 4 residues within 4Å: Chain I: C.108, H.111, C.179 Ligands: 8DG.19 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.108, I:H.111, I:C.179 ZN.20: 4 residues within 4Å: Chain J: C.108, H.111, C.179 Ligands: 8DG.13 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.108, J:H.111, J:C.179

10 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.2: 19 residues within 4Å: Chain A: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain B: A.87, L.130, G.131, L.132, S.133, K.134, R.137 Chain J: R.64 Ligands: ZN.1 23 PLIP interactions: 11 interactions with chain A, 10 interactions with chain B, 2 interactions with chain J Hydrogen bonds: A:Q.149, A:H.177, B:L.130, B:L.132, B:S.133, B:S.133, B:K.134 Water bridges: A:C.179, A:R.183, A:V.185, B:L.130 Salt bridges: A:H.111, A:H.111, A:E.150, A:R.183, A:R.183, B:K.134, B:K.134, B:K.134, B:R.137, J:K.60, J:R.64 pi-Stacking: A:H.110 8DG.3: 20 residues within 4Å: Chain A: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Chain E: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain F: R.64 Ligands: ZN.10 21 PLIP interactions: 11 interactions with chain A, 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: A:L.130, A:L.132, A:S.133, A:S.133, A:K.134, E:Q.149 Water bridges: A:L.130, A:S.133, E:H.177, E:C.179 Salt bridges: A:K.134, A:K.134, A:K.134, A:R.137, E:H.111, E:H.111, E:E.150, E:R.183, E:R.183, F:R.64 pi-Cation interactions: E:H.110 8DG.6: 21 residues within 4Å: Chain B: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain C: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Chain I: K.60, R.64 Ligands: ZN.4 23 PLIP interactions: 10 interactions with chain B, 2 interactions with chain I, 11 interactions with chain C Hydrogen bonds: B:H.110, B:Q.149, B:H.177, C:L.130, C:L.132, C:S.133, C:S.133, C:K.134 Water bridges: B:V.185, C:L.130, C:S.133 Salt bridges: B:H.111, B:H.111, B:E.150, B:R.183, B:R.183, I:K.60, I:R.64, C:K.134, C:K.134, C:K.134, C:R.137 pi-Stacking: B:H.110 8DG.8: 21 residues within 4Å: Chain C: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain D: G.85, A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Chain H: R.64 Ligands: ZN.5 23 PLIP interactions: 11 interactions with chain C, 10 interactions with chain D, 2 interactions with chain H Hydrogen bonds: C:H.111, C:Q.149, D:L.130, D:L.132, D:S.133, D:S.133, D:K.134 Water bridges: C:H.177, C:C.179, C:V.185, D:L.130 Salt bridges: C:H.111, C:H.111, C:E.150, C:R.183, C:R.183, D:K.134, D:K.134, D:K.134, D:R.137, H:K.60, H:R.64 pi-Stacking: C:H.110 8DG.9: 21 residues within 4Å: Chain D: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain E: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Chain G: R.64, K.67 Ligands: ZN.7 22 PLIP interactions: 9 interactions with chain D, 11 interactions with chain E, 2 interactions with chain G Hydrogen bonds: D:Q.149, D:H.177, E:L.130, E:L.132, E:S.133, E:S.133, E:K.134 Water bridges: D:C.179, E:L.130, E:S.133 Salt bridges: D:H.111, D:H.111, D:E.150, D:R.183, D:R.183, E:K.134, E:K.134, E:K.134, E:R.137, G:R.64, G:K.67 pi-Cation interactions: D:H.110 8DG.12: 19 residues within 4Å: Chain E: R.64 Chain F: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain G: A.87, L.130, G.131, L.132, S.133, K.134, R.137 Ligands: ZN.11 24 PLIP interactions: 10 interactions with chain G, 2 interactions with chain E, 12 interactions with chain F Hydrogen bonds: G:L.130, G:L.132, G:S.133, G:S.133, G:K.134, F:H.110, F:Q.149, F:H.177 Water bridges: G:L.130, F:C.179, F:R.183, F:V.185 Salt bridges: G:K.134, G:K.134, G:K.134, G:R.137, E:K.60, E:R.64, F:H.111, F:H.111, F:E.150, F:R.183, F:R.183 pi-Stacking: F:H.110 8DG.13: 20 residues within 4Å: Chain A: R.64 Chain F: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Chain J: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Ligands: ZN.20 21 PLIP interactions: 11 interactions with chain F, 9 interactions with chain J, 1 interactions with chain A Hydrogen bonds: F:L.130, F:L.132, F:S.133, F:S.133, F:K.134, J:H.110, J:Q.149 Water bridges: F:L.130, F:S.133, J:C.179 Salt bridges: F:K.134, F:K.134, F:K.134, F:R.137, J:H.111, J:H.111, J:E.150, J:R.183, J:R.183, A:R.64 pi-Cation interactions: J:H.110 8DG.16: 21 residues within 4Å: Chain D: K.60, R.64 Chain G: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain H: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Ligands: ZN.14 22 PLIP interactions: 2 interactions with chain D, 11 interactions with chain H, 9 interactions with chain G Salt bridges: D:K.60, D:R.64, H:K.134, H:K.134, H:K.134, H:R.137, G:H.111, G:H.111, G:E.150, G:R.183, G:R.183 Hydrogen bonds: H:L.130, H:L.132, H:S.133, H:S.133, H:K.134, G:Q.149, G:H.177 Water bridges: H:L.130, H:S.133, G:V.185 pi-Stacking: G:H.110 8DG.18: 21 residues within 4Å: Chain C: R.64 Chain H: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain I: G.85, A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Ligands: ZN.15 23 PLIP interactions: 11 interactions with chain H, 2 interactions with chain C, 10 interactions with chain I Hydrogen bonds: H:H.110, H:Q.149, I:L.130, I:L.132, I:S.133, I:S.133, I:K.134 Water bridges: H:H.177, H:C.179, H:V.185, I:L.130 Salt bridges: H:H.111, H:H.111, H:E.150, H:R.183, H:R.183, C:K.60, C:R.64, I:K.134, I:K.134, I:K.134, I:R.137 pi-Stacking: H:H.110 8DG.19: 21 residues within 4Å: Chain B: R.64, K.67 Chain I: C.108, H.110, H.111, V.148, Q.149, E.150, H.177, C.179, R.183, G.184 Chain J: A.87, F.89, L.130, G.131, L.132, S.133, K.134, R.137 Ligands: ZN.17 23 PLIP interactions: 10 interactions with chain I, 11 interactions with chain J, 2 interactions with chain B Hydrogen bonds: I:H.110, I:Q.149, I:H.177, J:L.130, J:L.132, J:S.133, J:S.133, J:K.134 Water bridges: I:C.179, J:L.130, J:S.133 Salt bridges: I:H.111, I:H.111, I:E.150, I:R.183, I:R.183, J:K.134, J:K.134, J:K.134, J:R.137, B:R.64, B:K.67 pi-Cation interactions: I:H.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, Y. et al., Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative. J.Biochem.(Tokyo) (2005)

Release Date

2005-07-19

Peptides

GTP cyclohydrolase I: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

GTP cyclohydrolase I

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