SMTL ID : 6zx9.1

Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: G.331, D.332, E.386, S.388, R.390, P.718 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.332, A:D.332, A:S.388, A:R.390 Water bridges: A:E.386, A:L.719 GOL.2: 5 residues within 4Å: Chain A: E.877, F.878, N.879, T.918, G.920 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.877, A:N.879, A:T.918, A:G.920 GOL.3: 5 residues within 4Å: Chain A: I.35, K.37, E.42, Y.44, F.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.37, A:Y.44 GOL.4: 2 residues within 4Å: Chain A: D.320, N.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.321 GOL.5: 7 residues within 4Å: Chain A: G.58, M.59, Y.60, I.1064, K.1065, S.1066, V.1067 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.1065, A:V.1067 Water bridges: A:M.59 GOL.6: 3 residues within 4Å: Chain A: D.363, I.726, L.818 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.726 Water bridges: A:D.363, A:L.818 GOL.7: 6 residues within 4Å: Chain B: C.55, H.96, L.97, D.312, L.313, C.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.96, B:L.313 GOL.9: 1 residues within 4Å: Chain C: E.208 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain C: H.204, H.250, C.255, H.257 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.204, C:H.250, C:C.255, C:H.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banchenko, S. et al., Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses. Plos Pathog. (2021)

Release Date

2021-07-21

Peptides

DNA damage-binding protein 1: A
DDB1- and CUL4-associated factor 1: B
Vpr protein fused to T4 lysozyme: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

DDB1- and CUL4-associated factor 1

Vpr protein fused to T4 lysozyme

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