MolNFT v1 · #73467 · protein

S. cerevisiae UBC12

3O2U · NEDD8-conjugating enzyme UBC12: “S. cerevisiae UBC12”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #73467 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3O2U
Type: protein
Length: 375 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NEDD8-conjugating enzyme UBC12
EC: 6.3.2.-
UniProt: P52491
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-)	protein	190	35% helix, 17% strand	P52491
B	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-)	protein	185	35% helix, 17% strand	P52491

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	508	0.69	0.80	47	empty
2	192	0.54	0.79	22	GOL
3	142	0.46	0.77	30	empty

Interfaces

1 interface between chains.

A–B · 839 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3O2U · S. cerevisiae Ubc12 · the same entry in another collection · chain A against A, TM-score 1.00
P52491 · AlphaFold monomer V2.0 prediction for NEDD8-conjugating enzyme UBC12 (P52491) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 P52491
Elsewhere: RCSB PDB 3O2U · PDBe 3O2U · UniProt P52491

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