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Crystal structure of ubiquitin charged UBE2N (UBE2N~UB) in complex with UBE2V2

Analyse Crystal structure of ubiquitin charged UBE2N (UBE2N~UB) in complex with UBE2V2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BBF
Type: protein
Length: 1,098 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 variant 2; Ubiquitin-conjugating enzyme E2 N…
EC: 2.3.2.23
UniProt: Q15819, P61088, P0CG48
Pockets: 12 · best druggability 0.55

Structure

x-ray diffraction · 8 distinct chains · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Ubiquitin-conjugating enzyme E2 variant 2	protein	142	20% helix, 20% strand	Q15819
B, E	Ubiquitin-conjugating enzyme E2 variant 2	protein	141	23% helix, 20% strand	Q15819
G	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	152	34% helix, 20% strand	P61088
D	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	149	35% helix, 20% strand	P61088
A	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	150	35% helix, 17% strand	P61088
I	Polyubiquitin-C	protein	74	20% helix, 35% strand	P0CG48
C	Polyubiquitin-C	protein	76	20% helix, 36% strand	P0CG48
F	Polyubiquitin-C	protein	73	21% helix, 36% strand	P0CG48

Pockets

12 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	221	0.55	0.78	25	empty
2	206	0.52	0.76	26	empty
3	168	0.46	0.75	28	empty
4	173	0.45	0.75	21	empty
5	100	0.36	0.75	18	empty

Interfaces

9 interfaces between chains.

H–G · 762 Å² buried · 4 hydrogen bonds · protein-protein
E–D · 728 Å² buried · 6 hydrogen bonds · protein-protein
B–A · 726 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 237 Å² buried · 3 hydrogen bonds · protein-protein
B–G · 178 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

7BBF · Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2 · the same entry in another collection · chain F against F, TM-score 1.00
Q15819 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 2 (Q15819) · 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 Q15819
Every structure of UniProt P61088
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 7BBF · PDBe 7BBF · UniProt Q15819 · UniProt P61088 · UniProt P0CG48

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