SMTL ID : 4zwe.3 (4 other biounits)

Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

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

DGT.1: 16 residues within 4Å: Chain A: Q.37, L.38, R.52, H.55, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.262 Hydrogen bonds: A:Q.37, A:R.52, A:Y.203, A:D.207, A:Y.262, A:Q.263 Salt bridges: A:R.52, A:R.94, A:R.94, A:H.98, A:H.103, A:H.103, A:H.121, A:H.121, A:K.200, A:R.254 pi-Stacking: A:H.258, A:H.258 DGT.2: 15 residues within 4Å: Chain A: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Chain B: R.221, F.225, R.240, K.242, N.246, K.411 Ligands: DGT.3 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.44, A:F.45 Hydrogen bonds: A:G.212, B:R.221, B:N.246 Salt bridges: A:H.264, A:H.264, A:K.265, A:K.265, B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:K.411 pi-Cation interactions: B:R.221, B:R.221 DGT.3: 7 residues within 4Å: Chain A: Y.43, V.44, V.266, R.339, K.343 Chain B: K.411 Ligands: DGT.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.339 Salt bridges: A:R.339, A:K.343, A:K.343, B:K.411, B:K.411 pi-Cation interactions: A:R.339 DGT.4: 13 residues within 4Å: Chain A: D.218, R.221, F.225, R.240, K.242, N.246, K.411 Chain B: V.44, F.45, R.260, H.264, K.265, V.266 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:V.44, B:F.45 Hydrogen bonds: B:R.260, A:D.218, A:R.221, A:N.246 Salt bridges: B:H.264, B:H.264, B:K.265, B:K.265, B:K.265, A:R.221, A:R.240, A:K.242, A:K.242, A:K.242, A:K.411 pi-Cation interactions: A:R.221, A:R.221 DGT.7: 10 residues within 4Å: Chain B: K.4, V.5, I.6, V.21, I.24, D.25, Q.30, R.33, F.53 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.6 Hydrogen bonds: B:Q.30, B:R.33 Salt bridges: B:K.4, B:K.4, B:K.4, B:D.25 DGT.8: 15 residues within 4Å: Chain B: Q.37, L.38, R.52, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.262 Hydrogen bonds: B:Q.37, B:L.38, B:R.52, B:D.199, B:Y.203, B:Y.203, B:Y.262, B:Q.263 Salt bridges: B:R.52, B:R.94, B:R.94, B:H.98, B:H.103, B:H.103, B:H.121, B:K.200, B:K.200, B:R.254 pi-Cation interactions: B:H.103

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: K.4 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: K.4 Ligands: DGT.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, C. et al., Impaired dNTPase Activity of SAMHD1 by Phosphomimetic Mutation of Thr-592. J.Biol.Chem. (2015)

Release Date

2015-09-02

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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