SMTL ID : 6z86.1 (1 other biounit)

human GTP cyclohydrolase I in complex with 7-deaza-GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.115, H.118, C.186 Ligands: QBQ.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.115, A:H.118, A:C.186, H2O.2 ZN.3: 4 residues within 4Å: Chain B: C.115, H.118, C.186 Ligands: QBQ.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.115, B:H.118, B:C.186, H2O.7 ZN.5: 4 residues within 4Å: Chain C: C.115, H.118, C.186 Ligands: QBQ.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.115, C:H.118, C:C.186, H2O.8 ZN.7: 4 residues within 4Å: Chain D: C.115, H.118, C.186 Ligands: QBQ.4 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.115, D:H.118, D:C.186, H2O.3 ZN.9: 4 residues within 4Å: Chain E: C.115, H.118, C.186 Ligands: QBQ.16 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.115, E:H.118, E:C.186, H2O.10 ZN.11: 4 residues within 4Å: Chain F: C.115, H.118, C.186 Ligands: QBQ.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.115, F:H.118, F:C.186, H2O.11 ZN.13: 4 residues within 4Å: Chain G: C.115, H.118, C.186 Ligands: QBQ.2 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.115, G:H.118, G:C.186, H2O.2 ZN.15: 4 residues within 4Å: Chain H: C.115, H.118, C.186 Ligands: QBQ.20 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.115, H:H.118, H:C.186, H2O.12 ZN.17: 4 residues within 4Å: Chain I: C.115, H.118, C.186 Ligands: QBQ.14 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:C.115, I:H.118, I:C.186, H2O.11 ZN.19: 4 residues within 4Å: Chain J: C.115, H.118, C.186 Ligands: QBQ.8 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:C.115, J:H.118, J:C.186, H2O.12

10 x QBQ: 7-deaza-GTP(Non-covalent)

QBQ.2: 20 residues within 4Å: Chain A: N.92, A.94, F.96, L.137, G.138, L.139, S.140, K.141, R.144 Chain E: R.71 Chain G: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Ligands: ZN.13 24 PLIP interactions: 14 interactions with chain A, 8 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: A:L.139, G:V.155 Hydrogen bonds: A:N.92, A:L.137, A:L.139, A:S.140, A:S.140, A:S.140, A:K.141, G:Q.156 Water bridges: A:K.141, A:R.144 Salt bridges: A:K.141, A:K.141, A:K.141, A:R.144, G:H.118, G:H.118, G:E.157, G:R.190, G:R.190, E:R.71, E:R.71 pi-Cation interactions: G:H.117 QBQ.4: 21 residues within 4Å: Chain B: N.92, A.94, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Chain C: R.71 Chain D: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Ligands: ZN.7 25 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D, 13 interactions with chain B Salt bridges: C:R.71, C:R.71, D:H.118, D:H.118, D:E.157, D:R.190, D:R.190, B:K.141, B:K.141, B:K.141, B:R.144 Hydrophobic interactions: D:V.155, B:L.139 Hydrogen bonds: D:Q.156, B:N.92, B:L.137, B:L.139, B:S.140, B:S.140, B:S.140, B:K.141 Water bridges: D:R.190, D:R.190, D:R.190, B:K.141 QBQ.6: 21 residues within 4Å: Chain A: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain B: R.71 Chain C: N.92, A.94, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Ligands: ZN.1 25 PLIP interactions: 10 interactions with chain A, 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:V.155, C:L.139 Hydrogen bonds: A:Q.156, C:N.92, C:L.137, C:L.139, C:S.140, C:S.140, C:S.140, C:K.141 Water bridges: A:R.190, A:V.192, C:L.137 Salt bridges: A:H.118, A:H.118, A:E.157, A:R.190, A:R.190, C:K.141, C:K.141, C:K.141, C:R.144, B:R.71, B:R.71 pi-Cation interactions: A:H.117 QBQ.8: 22 residues within 4Å: Chain D: N.92, A.94, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Chain F: K.67, R.71 Chain J: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Ligands: ZN.19 27 PLIP interactions: 12 interactions with chain D, 3 interactions with chain F, 12 interactions with chain J Hydrogen bonds: D:N.92, D:L.137, D:L.139, D:S.140, D:S.140, D:S.140, D:K.141, J:Q.156 Water bridges: D:R.144, J:H.184, J:R.190, J:R.190, J:V.192 Salt bridges: D:K.141, D:K.141, D:K.141, D:R.144, F:K.67, F:R.71, F:R.71, J:H.118, J:H.118, J:E.157, J:R.190, J:R.190 Hydrophobic interactions: J:V.155 pi-Cation interactions: J:H.117 QBQ.10: 20 residues within 4Å: Chain A: R.71 Chain B: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain E: N.92, A.94, F.96, L.137, G.138, L.139, S.140, K.141, R.144 Ligands: ZN.3 23 PLIP interactions: 11 interactions with chain E, 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: E:N.92, E:L.137, E:L.139, E:S.140, E:S.140, E:S.140, E:K.141, B:Q.156 Salt bridges: E:K.141, E:K.141, E:K.141, E:R.144, B:H.118, B:H.118, B:E.157, B:R.190, B:R.190, A:R.71, A:R.71 Hydrophobic interactions: B:V.155 Water bridges: B:H.118, A:R.71 pi-Cation interactions: B:H.117 QBQ.12: 20 residues within 4Å: Chain C: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain D: R.71 Chain F: N.92, A.94, F.96, L.137, G.138, L.139, S.140, K.141, R.144 Ligands: ZN.5 23 PLIP interactions: 9 interactions with chain C, 12 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: C:V.155, F:L.139 Hydrogen bonds: C:Q.156, F:N.92, F:L.137, F:L.139, F:S.140, F:S.140, F:S.140, F:K.141 Water bridges: C:H.118, C:V.192 Salt bridges: C:H.118, C:H.118, C:E.157, C:R.190, C:R.190, F:K.141, F:K.141, F:K.141, F:R.144, D:R.71, D:R.71 QBQ.14: 21 residues within 4Å: Chain G: N.92, A.94, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Chain H: R.71 Chain I: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Ligands: ZN.17 29 PLIP interactions: 13 interactions with chain I, 13 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: I:V.155, G:L.139 Hydrogen bonds: I:Q.156, G:N.92, G:L.137, G:L.139, G:S.140, G:S.140, G:S.140, G:K.141 Water bridges: I:H.118, I:H.184, I:R.190, I:R.190, I:R.190, G:L.137, H:R.71 Salt bridges: I:H.118, I:H.118, I:E.157, I:R.190, I:R.190, G:K.141, G:K.141, G:K.141, G:R.144, H:R.71, H:R.71 pi-Cation interactions: I:H.117 QBQ.16: 20 residues within 4Å: Chain E: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain G: R.71 Chain H: N.92, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Ligands: ZN.9 24 PLIP interactions: 8 interactions with chain E, 14 interactions with chain H, 2 interactions with chain G Hydrogen bonds: E:Q.156, H:N.92, H:L.137, H:L.139, H:S.140, H:S.140, H:S.140, H:K.141 Water bridges: E:H.184, H:R.144, H:R.144 Salt bridges: E:H.118, E:H.118, E:E.157, E:R.190, E:R.190, H:K.141, H:K.141, H:K.141, H:R.144, G:R.71, G:R.71 pi-Cation interactions: E:H.117 Hydrophobic interactions: H:L.139 QBQ.18: 21 residues within 4Å: Chain F: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain I: N.92, A.94, F.96, V.136, L.137, G.138, L.139, S.140, K.141, R.144 Chain J: R.71 Ligands: ZN.11 24 PLIP interactions: 2 interactions with chain J, 10 interactions with chain F, 12 interactions with chain I Salt bridges: J:R.71, J:R.71, F:H.118, F:H.118, F:E.157, F:R.190, F:R.190, I:K.141, I:K.141, I:K.141, I:R.144 Hydrophobic interactions: F:V.155 Hydrogen bonds: F:Q.156, I:N.92, I:L.137, I:L.139, I:S.140, I:S.140, I:S.140, I:K.141, I:K.141 Water bridges: F:R.190, F:V.192 pi-Cation interactions: F:H.117 QBQ.20: 20 residues within 4Å: Chain H: C.115, H.117, H.118, V.155, Q.156, E.157, H.184, R.190, G.191 Chain I: R.71 Chain J: N.92, A.94, F.96, L.137, G.138, L.139, S.140, K.141, R.144 Ligands: ZN.15 26 PLIP interactions: 16 interactions with chain J, 9 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: J:L.139, H:V.155 Hydrogen bonds: J:N.92, J:L.137, J:L.139, J:S.140, J:S.140, J:S.140, J:K.141, J:K.141, J:K.141, H:Q.156 Water bridges: J:K.141, J:R.144, H:H.184 Salt bridges: J:K.141, J:K.141, J:K.141, J:R.144, H:H.118, H:H.118, H:E.157, H:R.190, H:R.190, I:R.71 pi-Cation interactions: H:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ebenhoch, R. et al., A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-12-09

Peptides

GTP cyclohydrolase 1: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
O

F
P

G
Q

H
R

I
S

J
T

GTP cyclohydrolase 1

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