SMTL ID : 8gb1.1 (1 other biounit)

Crystal structure of SAMHD1 dimer bound to deoxyguanosine linked inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

2 x YWI: 5'-O-[(R)-(3-{[(1M)-3'-bromo[1,1'-biphenyl]-3-carbonyl]amino}propoxy)(hydroxy)phosphoryl]-2'-deoxyguanosine(Non-covalent)

YWI.1: 22 residues within 4Å: Chain A: Y.45, V.46, F.47, P.48, H.266, V.268, I.271, R.341, N.342, L.343, F.344, K.345, V.447 Chain B: K.6, V.7, I.8, V.23, I.26, D.27, Q.32, R.35, F.55 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.8, A:V.268 Hydrogen bonds: B:Q.32, B:R.35, A:R.341, A:R.341, A:K.345 Water bridges: B:D.27 Salt bridges: B:D.27, A:R.341 pi-Cation interactions: A:R.341 YWI.3: 23 residues within 4Å: Chain A: K.6, V.7, I.8, V.23, I.26, D.27, Q.32, R.35, F.55 Chain B: Y.45, V.46, F.47, P.48, H.266, K.267, V.268, I.271, R.341, N.342, L.343, F.344, K.345, V.447 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.8, B:V.268, B:N.342 Hydrogen bonds: A:K.6, A:Q.32, A:R.35, B:R.341, B:K.345 Water bridges: A:V.7, A:V.7, B:K.267, B:R.341 Salt bridges: A:K.6, A:D.27, B:R.341 pi-Cation interactions: B:R.341

2 x FE: FE (III) ION(Non-covalent)

FE.2: 7 residues within 4Å: Chain A: R.54, H.57, V.61, H.96, D.97, D.201, Y.205 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.57, A:H.96, A:D.97, A:D.201, H2O.4 FE.4: 7 residues within 4Å: Chain B: R.54, H.57, V.61, H.96, D.97, D.201, Y.205 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.57, B:H.96, B:D.97, B:D.201, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egleston, M. et al., Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding. Acs Chem.Biol. (2023)

Release Date

2023-06-07

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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