SMTL ID : 6u6y.2 (1 other biounit)

Human SAMHD1 bound to ribo(CGCCU)-oligonucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

2 x C- G- C: RNA CGCCU(Non-covalent)

C-G-C.1: 15 residues within 4Å: Chain A: Y.62, V.63, H.283, V.285, R.358, L.360 Chain B: K.23, V.24, I.25, H.32, I.43, D.44, Q.49, R.52, F.72 Protein-ligand interaction information (PLIP) not available C-G-C.2: 15 residues within 4Å: Chain A: K.23, V.24, I.25, N.26, H.32, I.43, D.44, Q.49, R.52, F.72 Chain B: Y.62, V.63, H.283, V.285, R.358 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: R.71, H.74, H.113, D.114, A.218 Ligands: DTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.74, A:H.113, A:D.114 ZN.5: 5 residues within 4Å: Chain B: H.74, H.113, D.114, A.218 Ligands: DTP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.74, B:H.113, B:D.114

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

DTP.4: 14 residues within 4Å: Chain A: Q.56, L.57, R.71, D.114, H.117, H.122, H.140, Y.222, D.226, H.277, Y.281, N.411, M.412 Ligands: ZN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.222, A:Y.281 Hydrogen bonds: A:Q.56, A:R.71, A:R.71, A:N.411 Water bridges: A:Q.56, A:H.69, A:H.122 Salt bridges: A:R.71, A:H.117, A:H.122, A:H.140 pi-Stacking: A:H.122, A:H.122, A:Y.281 DTP.6: 13 residues within 4Å: Chain B: Q.56, L.57, R.71, D.114, H.117, H.122, H.140, Y.222, D.226, H.277, Y.281, N.411 Ligands: ZN.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.222, B:Y.281 Hydrogen bonds: B:Q.56, B:R.71, B:N.411 Water bridges: B:H.69, B:D.226 Salt bridges: B:R.71, B:H.117, B:H.122, B:H.140 pi-Stacking: B:Y.281 pi-Cation interactions: B:H.122, B:H.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, C.H. et al., Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification. Nat Commun (2021)

Release Date

2020-09-02

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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