Research workbench

REV1 UBM2 domain complex with ubiquitin

Analyse REV1 UBM2 domain complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ASR
Type: protein
Length: 189 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; DNA repair protein REV1
EC: 2.7.7.-
UniProt: P0CG47, Q9UBZ9
Ligands: NI
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin	protein	76	24% helix, 33% strand	P0CG47
B	DNA repair protein REV1 (EC 2.7.7.-)	protein	39	67% helix, 0% strand	Q9UBZ9
C	Ubiquitin	protein	74	24% helix, 35% strand	P0CG47

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.49	0.82	15	NI

Interfaces

3 interfaces between chains.

A–B · 851 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 358 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 173 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6ASR · REV1 UBM2 domain complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
Q9UBZ9 · AlphaFold monomer V2.0 prediction for DNA repair protein REV1 (Q9UBZ9) · a predicted model of the same protein · chain B against A, TM-score 0.74

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 P0CG47
Every structure of UniProt Q9UBZ9
Elsewhere: RCSB PDB 6ASR · PDBe 6ASR · UniProt P0CG47 · UniProt Q9UBZ9

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