SMTL ID : 5ao1.1

Crystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: R.72, H.75, H.114, D.115, D.219 Ligands: DG3.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.75, A:H.114, A:D.115, A:D.219 FE.6: 6 residues within 4Å: Chain B: R.72, H.75, H.114, D.115, D.219 Ligands: DG3.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.75, B:H.114, B:D.115, B:D.219 FE.11: 6 residues within 4Å: Chain C: R.72, H.75, H.114, D.115, D.219 Ligands: DG3.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.75, C:H.114, C:D.115, C:D.219 FE.15: 6 residues within 4Å: Chain D: R.72, H.75, H.114, D.115, D.219 Ligands: DG3.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.75, D:H.114, D:D.115, D:D.219

8 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.2: 17 residues within 4Å: Chain A: R.72, H.75, H.114, D.115, H.118, H.123, G.127, H.141, E.142, D.219, K.220, Y.223, H.278, Y.282, N.288, M.413 Ligands: FE.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.282, A:Y.282 Hydrogen bonds: A:H.114, A:H.123, A:H.141, A:Y.223, A:N.288 Salt bridges: A:R.72, A:H.114, A:H.118, A:H.118, A:H.123, A:H.123, A:H.141, A:H.141, A:K.220 pi-Stacking: A:H.123 DG3.4: 12 residues within 4Å: Chain A: K.24, V.25, I.26, D.45, Q.50, R.53, F.73 Chain B: Y.63, V.64, V.286, R.359 Ligands: MG.5 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:R.359, A:K.24, A:K.24, A:Q.50, A:R.53 Salt bridges: B:R.359, A:K.24, A:K.24, A:D.45 pi-Cation interactions: B:R.359 Hydrophobic interactions: A:I.26 DG3.7: 15 residues within 4Å: Chain B: R.72, H.75, H.114, D.115, H.118, H.123, G.127, H.141, E.142, D.219, K.220, Y.223, H.278, Y.282 Ligands: FE.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.282, B:Y.282 Hydrogen bonds: B:H.123, B:E.142, B:N.288 Water bridges: B:H.123, B:H.123, B:N.412, B:N.412, B:N.412 Salt bridges: B:R.72, B:H.114, B:H.118, B:H.118, B:H.123, B:H.123, B:H.141, B:K.220 pi-Stacking: B:H.123 DG3.8: 15 residues within 4Å: Chain A: Y.63, V.64, V.286, R.359, L.361 Chain B: K.24, V.25, I.26, V.41, I.44, D.45, Q.50, R.53, F.73 Ligands: MG.10 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.26 Hydrogen bonds: B:K.24, B:K.24, B:Q.50, B:R.53, A:R.359 Salt bridges: B:K.24, B:K.24, B:K.24, B:D.45, A:R.359 pi-Cation interactions: A:R.359 DG3.12: 18 residues within 4Å: Chain C: R.72, H.75, H.114, D.115, H.118, H.123, G.127, H.141, E.142, D.219, K.220, Y.223, H.278, Y.282, N.288, D.291, M.413 Ligands: FE.11 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.282, C:Y.282 Hydrogen bonds: C:H.114, C:H.123, C:Y.223, C:D.291 Salt bridges: C:R.72, C:H.114, C:H.118, C:H.118, C:H.123, C:H.123, C:H.141, C:K.220 pi-Stacking: C:H.123 DG3.13: 15 residues within 4Å: Chain C: K.24, V.25, I.26, V.41, I.44, D.45, Q.50, R.53, F.73 Chain D: Y.63, V.64, V.286, R.359, L.361 Ligands: MG.14 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.26 Hydrogen bonds: C:K.24, C:K.24, C:Q.50, C:R.53 Water bridges: C:Q.50 Salt bridges: C:K.24, C:K.24, C:D.45, D:R.359 pi-Cation interactions: D:R.359 DG3.16: 15 residues within 4Å: Chain D: R.72, H.75, H.114, D.115, H.118, H.123, G.127, H.141, E.142, D.219, K.220, Y.223, H.278, N.288 Ligands: FE.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:N.288 Water bridges: D:H.123, D:H.123, D:H.123, D:K.220 Salt bridges: D:R.72, D:H.114, D:H.118, D:H.118, D:H.123, D:H.123, D:H.141, D:K.220 pi-Stacking: D:H.123 DG3.17: 15 residues within 4Å: Chain C: Y.63, V.64, V.286, R.359, L.361 Chain D: K.24, V.25, I.26, V.41, I.44, D.45, Q.50, R.53, F.73 Ligands: MG.20 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.26 Hydrogen bonds: D:K.24, D:K.24, D:Q.50, D:R.53, C:R.359 Salt bridges: D:K.24, D:K.24, D:D.45, C:R.359 pi-Cation interactions: C:R.359

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: I.233, Q.234, R.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.234 Salt bridges: A:R.280 SO4.9: 4 residues within 4Å: Chain B: K.347, R.350, E.351, K.354 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.350, B:K.354 SO4.18: 3 residues within 4Å: Chain D: K.347, R.350, E.351 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.350 SO4.19: 2 residues within 4Å: Chain D: K.377, R.378 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.378 Salt bridges: D:R.378

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.5: 1 residues within 4Å: Ligands: DG3.4 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: V.286, L.361 Ligands: DG3.8 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: DG3.13 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: DG3.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnold, L.H. et al., Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction. Plos Pathog. (2015)

Release Date

2015-10-14

Peptides

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1