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UBE2D1 in complex with ubiquitin variant UBV.D1.1

Analyse UBE2D1 in complex with ubiquitin variant UBV.D1.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6D4P
Type: protein
Length: 223 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 D1; Ubiquitin variant UBV.D1.1
EC: 2.3.2.23, 2.3.2.24
UniProt: P51668, Q59EM9
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 D1 (EC 2.3.2.23, 2.3.2.24)	protein	149	38% helix, 17% strand	P51668
C	Ubiquitin variant UBV.D1.1	protein	74	24% helix, 38% strand	Q59EM9

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	126	0.52	0.81	21	empty

Interfaces

1 interface between chains.

A–C · 792 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6D4P · Ube2D1 in complex with ubiquitin variant Ubv.D1.1 · the same entry in another collection · chain A against A, TM-score 1.00
P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · 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 P51668
Every structure of UniProt Q59EM9
Elsewhere: RCSB PDB 6D4P · PDBe 6D4P · UniProt P51668 · UniProt Q59EM9

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