MolNFT v1 · #159922 · protein

Crystal structure of mavc in complex with ub-UBE2N

6P5B: “Crystal structure of mavc in complex with ub-UBE2N”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #159922 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6P5B
Type: protein
Length: 613 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mavc; Ubiquitin-conjugating enzyme E2 N; Ubiquitin
EC: 2.3.2.23
UniProt: A0A2S6F4I5, P61088, P0CG48
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mavc	protein	388	51% helix, 14% strand	A0A2S6F4I5
C	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	150	32% helix, 19% strand	P61088
E	Ubiquitin	protein	75	24% helix, 32% strand	P0CG48

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.78	0.87	61	empty
2	1004	0.78	0.80	98	empty
3	220	0.53	0.77	39	empty
4	114	0.39	0.75	25	empty

Interfaces

3 interfaces between chains.

A–C · 1401 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 1311 Å² buried · 28 hydrogen bonds · protein-protein
C–E · 248 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6P5B · Crystal Structure of MavC in Complex with Ub-UbE2N · the same entry in another collection · chain A against A, TM-score 1.00
P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 A0A2S6F4I5
Every structure of UniProt P61088
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 6P5B · PDBe 6P5B · UniProt A0A2S6F4I5 · UniProt P61088 · UniProt P0CG48

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