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Crystal structure of UFD2 in complex with the ubiquitin-like (ubl) domain of RAD23

Analyse Crystal structure of UFD2 in complex with the ubiquitin-like (ubl) domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M62
Type: protein
Length: 1,027 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin conjugation factor E4; UV excision repair protein RAD23
UniProt: P54860, P32628
Ligands: K
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin conjugation factor E4	protein	955	67% helix, 2% strand	P54860
B	UV excision repair protein RAD23	protein	72	18% helix, 29% strand	P32628

Ligands and binding sites

K · Potassium ion · metal · chains A
1PE · Pentaethylene glycol · additive · chains A

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

Pockets

7 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	288	0.63	0.80	36	empty
2	128	0.59	0.84	22	empty
3	267	0.56	0.77	32	empty
4	264	0.50	0.74	38	empty
5	108	0.43	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 666 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3M62 · Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23 · the same entry in another collection · chain A against A, TM-score 1.00
P32628 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 (P32628) · a predicted model of the same protein · chain B against A, TM-score 0.96
P54860 · AlphaFold monomer V2.0 prediction for E4 ubiquitin-protein ligase UFD2 (P54860) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P54860
Every structure of UniProt P32628
Elsewhere: RCSB PDB 3M62 · PDBe 3M62 · UniProt P54860 · UniProt P32628

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