MolNFT v1 · #154744 · protein

Crystal structure of mavc-UBE2N-ub

6KL4: “Crystal structure of mavc-UBE2N-ub”. X-ray diffraction, 3 pockets (best druggability 0.79). MolNFT v1 #154744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KL4
Type: protein
Length: 602 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mavc; Ubiquitin-conjugating enzyme E2 N; Ub
EC: 2.3.2.23
UniProt: A0A2S6F4I5, P61088
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mavc	protein	377	47% helix, 15% strand	A0A2S6F4I5
B	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	151	34% helix, 17% strand	P61088
C	Ub	protein	74	26% helix, 30% strand	—

Pockets

3 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	1003	0.79	0.81	89	empty
2	554	0.74	0.82	76	empty
3	176	0.51	0.78	20	empty

Interfaces

3 interfaces between chains.

A–C · 1319 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1245 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 203 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6KL4 · Crystal structure of MavC-UBE2N-Ub · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.95

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
Elsewhere: RCSB PDB 6KL4 · PDBe 6KL4 · UniProt A0A2S6F4I5 · UniProt P61088

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