MolNFT v1 · #71170 · protein

Crystal structure of UFD2 in complex with the ubiquitin-like (ubl) domain of DSK2

3M63 · Ubiquitin conjugation factor E4: “Crystal structure of UFD2 in complex with the ubiquitin-like (ubl) domain of DSK2”. X-ray diffraction, 1 ligand (K), 9 pockets (best druggability 0.60). MolNFT v1 #71170 on GenesisL1: 3D structure…

PDB: 3M63
Type: protein
Length: 1,025 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin conjugation factor E4; Ubiquitin domain-containing protein DSK2
UniProt: P54860, P48510
Ligands: K
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin conjugation factor E4	protein	953	66% helix, 2% strand	P54860
B	Ubiquitin domain-containing protein DSK2	protein	72	17% helix, 24% strand	P48510

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

9 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	206	0.60	0.81	34	empty
2	307	0.58	0.77	37	empty
3	130	0.47	0.78	27	empty
4	137	0.45	0.77	28	empty
5	87	0.40	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 594 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3M63 · Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 · the same entry in another collection · chain A against A, TM-score 1.00
P48510 · AlphaFold monomer V2.0 prediction for ubiquitin domain-containing protein DSK2 (P48510) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P48510
Elsewhere: RCSB PDB 3M63 · PDBe 3M63 · UniProt P54860 · UniProt P48510

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