SMTL ID : 6oiy.1

Structure of Escherichia coli bound to dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-hexamer

Ligands

6 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)(Covalent)

DGT.1: 15 residues within 4Å: Chain A: Q.53, V.54, H.126, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Chain B: R.442 Ligands: MN.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.391 Hydrogen bonds: A:Q.53, A:V.54, A:Y.272, A:Y.272, B:R.442 Water bridges: A:D.118, A:D.268 Salt bridges: A:K.211, A:K.211, A:K.232, A:K.232, A:E.400 pi-Stacking: A:F.391, A:F.391 pi-Cation interactions: A:F.391 DGT.3: 16 residues within 4Å: Chain B: Q.53, V.54, H.126, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 Chain C: R.433, R.442 Ligands: MN.4 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.54, B:F.391 Hydrogen bonds: B:V.54, B:N.186, B:Y.212, B:Y.272, C:R.433, C:R.433, C:R.442 Water bridges: B:Y.212, B:K.231 Salt bridges: B:H.126, B:K.211, B:K.211, B:K.232, B:K.232, B:E.400 pi-Stacking: B:F.391, B:F.391 pi-Cation interactions: B:F.391 DGT.5: 18 residues within 4Å: Chain A: R.433, R.442 Chain C: Q.53, V.54, R.66, H.126, N.186, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Ligands: MN.6 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.391 Hydrogen bonds: C:Q.53, C:V.54, C:R.66, C:E.184, C:N.186, C:N.186, A:R.433, A:R.442 Salt bridges: C:H.126, C:K.211, C:K.211, C:K.232, C:K.232, C:E.400 pi-Stacking: C:F.391, C:F.391 DGT.8: 17 residues within 4Å: Chain D: Q.53, V.54, H.126, E.184, N.186, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Chain F: R.433, R.442 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.391 Hydrogen bonds: D:Q.53, D:V.54, D:N.186, D:Y.212, F:R.433, F:R.442 Salt bridges: D:H.126, D:K.211, D:K.211, D:K.232, D:K.232, D:K.232, D:E.400 pi-Stacking: D:F.391, D:F.391 DGT.9: 17 residues within 4Å: Chain D: R.433, R.442 Chain E: Q.53, V.54, H.126, N.186, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Ligands: MN.10 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.391 Hydrogen bonds: E:V.54, E:N.186, E:N.186, E:Y.212, E:Y.272, D:R.433, D:R.442 Water bridges: E:D.118 Salt bridges: E:H.126, E:K.211, E:K.211, E:K.232, E:K.232, E:K.232, E:E.400 pi-Stacking: E:F.391, E:F.391 DGT.11: 18 residues within 4Å: Chain E: R.433, R.442 Chain F: Q.53, V.54, H.126, E.184, N.186, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Ligands: MN.12 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:F.391 Hydrogen bonds: F:Q.53, F:V.54, F:N.186, E:R.433, E:R.433, E:R.442 Water bridges: F:K.211 Salt bridges: F:H.126, F:K.211, F:K.211, F:K.232, F:K.232, F:E.400 pi-Stacking: F:F.391, F:F.391 pi-Cation interactions: F:H.126

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: H.69, H.117, D.118, D.268 Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MN.4: 5 residues within 4Å: Chain B: H.69, H.117, D.118, D.268 Ligands: DGT.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.117, B:D.268 MN.6: 5 residues within 4Å: Chain C: H.69, H.117, D.118, D.268 Ligands: DGT.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.268 MN.7: 4 residues within 4Å: Chain D: H.69, H.117, D.118, D.268 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.268, H2O.1 MN.10: 5 residues within 4Å: Chain E: H.69, H.117, D.118, D.268 Ligands: DGT.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.117, E:D.268 MN.12: 6 residues within 4Å: Chain F: H.69, H.117, D.118, D.268, Y.272 Ligands: DGT.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-05-15

Peptides

Deoxyguanosinetriphosphate triphosphohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Deoxyguanosinetriphosphate triphosphohydrolase

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