SMTL ID : 7tu7.1

Structure of the L. blandensis dGTPase H125A mutant bound to dGTP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

DGT.1: 18 residues within 4Å: Chain A: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.2, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.74, A:V.75, A:N.183, A:N.183, A:Y.214, A:D.275 Salt bridges: A:R.87, A:K.213, A:K.231, A:K.231, A:E.391 pi-Stacking: A:Y.382, A:Y.382 pi-Cation interactions: A:Y.382 DGT.5: 18 residues within 4Å: Chain B: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.6, MG.7, MG.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.74, B:V.75, B:N.183, B:N.183, B:D.275, B:Y.279 Salt bridges: B:R.87, B:K.213, B:K.231, B:K.231, B:E.391 pi-Stacking: B:Y.382, B:Y.382 pi-Cation interactions: B:Y.382 DGT.9: 18 residues within 4Å: Chain C: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.10, MG.11, MG.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.74, C:V.75, C:N.183, C:N.183, C:Y.214, C:D.275 Salt bridges: C:R.87, C:K.213, C:K.231, C:K.231, C:E.391 pi-Stacking: C:Y.382, C:Y.382 pi-Cation interactions: C:Y.382 DGT.13: 18 residues within 4Å: Chain D: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.14, MG.15, MG.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.74, D:V.75, D:N.183, D:N.183, D:D.275, D:Y.279 Salt bridges: D:R.87, D:K.213, D:K.231, D:K.231, D:E.391 pi-Stacking: D:Y.382, D:Y.382 pi-Cation interactions: D:Y.382 DGT.17: 18 residues within 4Å: Chain E: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.18, MG.19, MG.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.74, E:V.75, E:N.183, E:N.183, E:Y.214, E:D.275 Salt bridges: E:R.87, E:K.213, E:K.231, E:K.231, E:E.391 pi-Stacking: E:Y.382, E:Y.382 pi-Cation interactions: E:Y.382 DGT.21: 18 residues within 4Å: Chain F: Q.74, V.75, R.87, H.90, D.139, N.183, K.213, Y.214, K.231, D.275, Y.279, D.283, Y.382, V.387, E.391 Ligands: MG.22, MG.23, MG.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.74, F:V.75, F:N.183, F:N.183, F:D.275, F:Y.279 Salt bridges: F:R.87, F:K.213, F:K.231, F:K.231, F:E.391 pi-Stacking: F:Y.382, F:Y.382 pi-Cation interactions: F:Y.382

18 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.90, H.138, D.139, D.275 Ligands: DGT.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.90, A:H.138, A:D.139, A:D.275, A:D.275 MG.3: 2 residues within 4Å: Chain A: D.139 Ligands: DGT.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.139 MG.4: 2 residues within 4Å: Chain A: K.213 Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: H.90, H.138, D.139, D.275 Ligands: DGT.5 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.90, B:H.138, B:D.139, B:D.275, B:D.275 MG.7: 2 residues within 4Å: Chain B: D.139 Ligands: DGT.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.139 MG.8: 2 residues within 4Å: Chain B: K.213 Ligands: DGT.5 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain C: H.90, H.138, D.139, D.275 Ligands: DGT.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.90, C:H.138, C:D.139, C:D.275, C:D.275 MG.11: 2 residues within 4Å: Chain C: D.139 Ligands: DGT.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.139 MG.12: 2 residues within 4Å: Chain C: K.213 Ligands: DGT.9 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain D: H.90, H.138, D.139, D.275 Ligands: DGT.13 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.90, D:H.138, D:D.139, D:D.275, D:D.275 MG.15: 2 residues within 4Å: Chain D: D.139 Ligands: DGT.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.139 MG.16: 2 residues within 4Å: Chain D: K.213 Ligands: DGT.13 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain E: H.90, H.138, D.139, D.275 Ligands: DGT.17 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.90, E:H.138, E:D.139, E:D.275, E:D.275 MG.19: 2 residues within 4Å: Chain E: D.139 Ligands: DGT.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.139 MG.20: 2 residues within 4Å: Chain E: K.213 Ligands: DGT.17 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain F: H.90, H.138, D.139, D.275 Ligands: DGT.21 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.90, F:H.138, F:D.139, F:D.275, F:D.275 MG.23: 2 residues within 4Å: Chain F: D.139 Ligands: DGT.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.139 MG.24: 2 residues within 4Å: Chain F: K.213 Ligands: DGT.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klemm, B.P. et al., High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J.Biol.Chem. (2022)

Release Date

2022-06-01

Peptides

dGTP triphosphohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

dGTP triphosphohydrolase

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