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Dimeric structure of the catalytic domain of the human ubiquitin- conjugating enzyme UBE2S L114E varaiant

Analyse Dimeric structure of the catalytic domain of the human ubiquitin- conjugating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AHF
Type: protein
Length: 297 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 S
EC: 2.3.2.23
UniProt: Q16763
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23)	protein	148	39% helix, 17% strand	Q16763
A	Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23)	protein	149	40% helix, 17% strand	Q16763

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains B, A
GOL · Glycerol · additive · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	413	0.71	0.82	57	GOL
2	57	0.45	0.84	18	empty
3	57	0.26	0.73	15	empty

Interfaces

1 interface between chains.

B–A · 1013 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 disulfide (additive adduct, disulfide).

Compared structures

7AHF · Dimeric structure of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S… · the same entry in another collection · chain B against B, TM-score 1.00
Q16763 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 S (Q16763) · a predicted model of the same protein · chain B 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 Q16763
Elsewhere: RCSB PDB 7AHF · PDBe 7AHF · UniProt Q16763

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