MolNFT v1 · #189241 · protein

Cryoem structure of DDB1-vprbp-vpr-UNG2(94-313) complex

7V7C · DDB1- and CUL4-associated factor 1: “Cryoem structure of DDB1-vprbp-vpr-UNG2(94-313) complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #189241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7V7C
Type: protein
Length: 5,084 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DDB1- and CUL4-associated factor 1; DNA damage-binding protein 1; Protein vpr; Uracil-DNA…
EC: 2.7.11.1, 3.2.2.27
UniProt: Q9Y4B6, Q16531, B2CPZ1, P13051
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 4 distinct chains · 24% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	DDB1- and CUL4-associated factor 1 (EC 2.7.11.1)	protein	1110	42% helix, 13% strand	Q9Y4B6
B, F	DNA damage-binding protein 1	protein	1133	4% helix, 41% strand	Q16531
C, G	Protein vpr	protein	79	53% helix, 1% strand	B2CPZ1
D, H	Uracil-DNA glycosylase (EC 3.2.2.27)	protein	220	28% helix, 5% strand	P13051

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	908	0.85	0.87	79	empty
2	1109	0.85	0.86	79	empty
3	799	0.84	0.87	96	empty
4	997	0.82	0.83	87	empty
5	1165	0.82	0.83	116	empty

Interfaces

14 interfaces between chains.

A–E · 3967 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 3625 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 3622 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 1754 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 1751 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7V7C · CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex · the same entry in another collection · chain H against H, TM-score 1.00
P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain D against A, TM-score 0.93
Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain F against A, TM-score 0.93
Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain E against A, TM-score 0.62

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y4B6
Every structure of UniProt Q16531
Every structure of UniProt B2CPZ1
Every structure of UniProt P13051
Elsewhere: RCSB PDB 7V7C · PDBe 7V7C · UniProt Q9Y4B6 · UniProt Q16531 · UniProt B2CPZ1 · UniProt P13051

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