SMTL ID : 4zwg.2 (2 other biounits)

Crystal structure of the GTP-dATP-bound catalytic core of SAMHD1 phosphomimetic T592E mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 16 residues within 4Å: Chain A: Q.37, L.38, R.52, R.94, 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:Q.263 Water bridges: A:R.254 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.103, A:H.103, A:H.258, A:H.258 DTP.3: 7 residues within 4Å: Chain A: R.221, F.225, R.240, K.242, N.246, K.411 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.221, A:N.246, A:N.246 Water bridges: A:K.411, A:K.411 Salt bridges: 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 DTP.8: 5 residues within 4Å: Chain B: R.221, R.240, K.242, N.246, K.411 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.221, B:N.246, B:N.246 Salt bridges: 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 DTP.9: 16 residues within 4Å: Chain B: Q.37, L.38, R.52, H.55, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.262 Hydrogen bonds: B:Q.37, B:R.52, B:N.95 Water bridges: B:R.94, B:K.200 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-Stacking: B:H.258, B:H.258

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

GTP.2: 13 residues within 4Å: Chain A: Y.43, V.44, V.266, R.339 Chain B: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Ligands: MG.7 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.5, B:Q.30, B:R.33 Water bridges: B:K.4, B:K.4, B:K.4 Salt bridges: B:K.4, B:K.4, B:K.4, B:D.25, A:R.339 pi-Cation interactions: A:R.339 GTP.6: 14 residues within 4Å: Chain A: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain B: Y.43, V.44, K.265, V.266, R.339 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.5, A:Q.30, A:R.33 Water bridges: A:K.4, A:K.4, A:K.4 Salt bridges: A:K.4, A:K.4, A:K.4, A:D.25, B:K.265, B:R.339 pi-Cation interactions: B:R.339

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: K.411 Ligands: DTP.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: K.4 Ligands: GTP.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: K.4 Ligands: GTP.2 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
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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