SMTL ID : 4rxo.2 (1 other biounit)

The structure of GTP-bound SAMHD1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: R.77, H.80, H.119, D.120, D.224 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.80, A:H.119, A:D.120, A:D.224 ZN.4: 6 residues within 4Å: Chain B: R.77, H.80, H.119, D.120, D.224 Ligands: PO4.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.80, B:H.119, B:D.120, B:D.224

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

GTP.2: 13 residues within 4Å: Chain A: Y.68, V.69, V.291, R.364, L.366 Chain B: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:V.30, B:Q.55, B:R.58, A:R.364 Water bridges: B:K.29, B:N.32, B:D.50, B:Q.55, A:R.364, A:K.368, A:K.368 Salt bridges: B:K.29, B:K.29, B:K.29, B:D.50, A:R.364 pi-Cation interactions: A:R.364 GTP.5: 13 residues within 4Å: Chain A: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 Chain B: Y.68, V.69, V.291, R.364, L.366 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.30, A:Q.55, A:R.58, B:R.364 Water bridges: A:N.32 Salt bridges: A:K.29, A:K.29, A:K.29, A:D.50, B:R.364 pi-Cation interactions: B:R.364

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: R.77, H.80, H.119, D.120, H.123, H.128, H.146, D.224 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.224 Water bridges: A:R.77, A:R.77 Salt bridges: A:R.77, A:H.123, A:H.128, A:H.146 PO4.6: 9 residues within 4Å: Chain B: R.77, H.80, D.120, H.123, H.128, H.146, D.224, Y.228 Ligands: ZN.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.224 Water bridges: B:R.77, B:R.77 Salt bridges: B:R.77, B:H.123, B:H.128, B:H.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, C.F. et al., The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-11

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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