SMTL ID : 6u6x.1 (1 other biounit)

Human SAMHD1 bound to deoxyribo(C*G*C*C*T)-oligonucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

2 x SC- GS- SC- SC: DNA SC-GS-SC-SC-DT(Non-covalent)

SC-GS-SC-SC.1: 19 residues within 4Å: Chain A: Y.62, V.63, R.278, R.279, H.283, K.284, V.285, R.358, L.360 Chain B: K.23, V.24, I.25, N.26, H.32, I.43, D.44, Q.49, R.52, F.72 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.25 Hydrogen bonds: B:Q.49, B:R.52, A:R.358, A:R.278, A:H.283, A:K.284 Salt bridges: B:D.44 pi-Cation interactions: A:R.358 SC-GS-SC-SC.2: 20 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, R.278, R.279, H.283, K.284, V.285, R.358, L.360, K.362 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.358, A:Q.49, A:R.52, B:H.283, B:K.284 pi-Cation interactions: B:R.358 Hydrophobic interactions: A:I.25 Salt bridges: A:D.44

2 x ZN: ZINC ION(Non-covalent)

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

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
A

B
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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