MolNFT v1 · #57291 · protein

UBCH5B~UBIQUITIN conjugate

3A33 · Ubiquitin-conjugating enzyme E2 D2: “UBCH5B~UBIQUITIN conjugate”. X-ray diffraction, 1 pocket (best druggability 0.59). MolNFT v1 #57291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A33
Type: protein
Length: 226 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 D2; Ubiquitin
EC: 6.3.2.19
UniProt: P62837, P62988
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19)	protein	150	37% helix, 18% strand	P62837
B	Ubiquitin	protein	76	24% helix, 33% strand	P62988

Ligands and binding sites

GOL · Glycerol · additive · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	203	0.59	0.81	32	GOL

Interfaces

1 interface between chains.

A–B · 479 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3A33 · UbcH5b~Ubiquitin Conjugate · the same entry in another collection · chain A against A, TM-score 1.00
P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P62837
Every structure of UniProt P62988
Elsewhere: RCSB PDB 3A33 · PDBe 3A33 · UniProt P62837 · UniProt P62988

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.