MolNFT v1 · #26854 · protein

Crystal structure of UBCH5C

1X23 · Ubiquitin-conjugating enzyme E2 D3: “Crystal structure of UBCH5C”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #26854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1X23
Type: protein
Length: 611 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 D3
EC: 6.3.2.19
UniProt: P61077
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19)	protein	153	37% helix, 18% strand	P61077
B, C	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19)	protein	152	36% helix, 20% strand	P61077
D	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19)	protein	154	36% helix, 17% strand	P61077

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.78	0.85	62	empty
2	694	0.77	0.82	64	empty
3	572	0.71	0.79	76	empty
4	71	0.59	0.90	21	empty
5	52	0.26	0.74	12	empty

Interfaces

5 interfaces between chains.

A–D · 612 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 595 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 591 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 501 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 492 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1X23 · Crystal structure of ubch5c · the same entry in another collection · chain A against A, TM-score 1.00
P61077 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D3 (P61077) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P61077
Elsewhere: RCSB PDB 1X23 · PDBe 1X23 · UniProt P61077

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