SMTL ID : 7u67.1

Structure of E. coli dGTPase bound to T7 bacteriophage protein Gp1.2 and GTP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 14 residues within 4Å: Chain A: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 Chain B: G.6, R.7 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Q.53, A:N.186, A:Y.212, A:Y.212, A:Y.212, A:Y.272, B:G.6, B:R.7, B:R.7 Salt bridges: A:K.211, A:K.232, A:E.400, B:R.7 pi-Stacking: A:F.391, A:F.391 pi-Cation interactions: A:F.391, B:R.7, B:R.7 GTP.3: 14 residues within 4Å: Chain C: G.6, R.7 Chain H: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 18 PLIP interactions: 12 interactions with chain H, 6 interactions with chain C Hydrogen bonds: H:Q.53, H:N.186, H:Y.212, H:Y.212, H:Y.272, H:Y.272, C:G.6, C:R.7, C:R.7 Salt bridges: H:K.211, H:K.232, H:E.400, C:R.7 pi-Stacking: H:F.391, H:F.391 pi-Cation interactions: H:F.391, C:R.7, C:R.7 GTP.5: 14 residues within 4Å: Chain D: G.6, R.7 Chain I: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 18 PLIP interactions: 12 interactions with chain I, 6 interactions with chain D Hydrogen bonds: I:Q.53, I:N.186, I:Y.212, I:Y.212, I:Y.212, I:Y.272, D:G.6, D:R.7, D:R.7 Salt bridges: I:K.211, I:K.232, I:E.400, D:R.7 pi-Stacking: I:F.391, I:F.391 pi-Cation interactions: I:F.391, D:R.7, D:R.7 GTP.7: 14 residues within 4Å: Chain E: G.6, R.7 Chain J: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 18 PLIP interactions: 6 interactions with chain E, 12 interactions with chain J Hydrogen bonds: E:G.6, E:R.7, E:R.7, J:Q.53, J:N.186, J:Y.212, J:Y.212, J:Y.272, J:Y.272 Salt bridges: E:R.7, J:K.211, J:K.232, J:E.400 pi-Cation interactions: E:R.7, E:R.7, J:F.391 pi-Stacking: J:F.391, J:F.391 GTP.9: 14 residues within 4Å: Chain F: G.6, R.7 Chain K: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 18 PLIP interactions: 12 interactions with chain K, 6 interactions with chain F Hydrogen bonds: K:Q.53, K:N.186, K:Y.212, K:Y.212, K:Y.272, K:Y.272, F:G.6, F:R.7, F:R.7 Salt bridges: K:K.211, K:K.232, K:E.400, F:R.7 pi-Stacking: K:F.391, K:F.391 pi-Cation interactions: K:F.391, F:R.7, F:R.7 GTP.11: 14 residues within 4Å: Chain G: G.6, R.7 Chain L: Q.53, V.54, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 18 PLIP interactions: 12 interactions with chain L, 6 interactions with chain G Hydrogen bonds: L:Q.53, L:N.186, L:Y.212, L:Y.212, L:Y.212, L:Y.272, G:G.6, G:R.7, G:R.7 Salt bridges: L:K.211, L:K.232, L:E.400, G:R.7 pi-Stacking: L:F.391, L:F.391 pi-Cation interactions: L:F.391, G:R.7, G:R.7

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:H.117, A:D.268, A:D.268 MG.4: 3 residues within 4Å: Chain H: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.69, H:H.117, H:D.268, H:D.268 MG.6: 3 residues within 4Å: Chain I: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.69, I:H.117, I:D.268, I:D.268 MG.8: 3 residues within 4Å: Chain J: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.69, J:H.117, J:D.268, J:D.268 MG.10: 3 residues within 4Å: Chain K: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.69, K:H.117, K:D.268, K:D.268 MG.12: 3 residues within 4Å: Chain L: H.69, H.117, D.268 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.69, L:H.117, L:D.268, L:D.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klemm, B.P. et al., Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-31

Peptides

Deoxyguanosinetriphosphate triphosphohydrolase: AHIJKL
Inhibitor of dGTPase: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
D

I
C

J
B

K
F

L
E

B
G

C
J

D
I

E
H

F
L

G
K

Deoxyguanosinetriphosphate triphosphohydrolase

Inhibitor of dGTPase

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