SMTL ID : 6z86.2 (1 other biounit)

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

Coordinates

PDB Format Compare

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

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

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

B
F

C
G

D
H

E
I

F
J

G
K

H
L

I
M

J
N

GTP cyclohydrolase 1

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