MolNFT v1 · #154587 · protein

Crystal structure of MAVC/UBE2N-ub complex

6KG6: “Crystal structure of MAVC/UBE2N-ub complex”. X-ray diffraction, 3 pockets (best druggability 0.79). MolNFT v1 #154587 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KG6
Type: protein
Length: 605 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mavc; Ubiquitin-40S ribosomal protein S27A; Ubiquitin-conjugating enzyme E2 N
EC: 2.3.2.23
UniProt: A0A2S6F4I5, J3QTR3, P61088
Pockets: 3 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Mavc	protein	379	50% helix, 15% strand	A0A2S6F4I5
C	Ubiquitin-40S ribosomal protein S27A	protein	75	24% helix, 35% strand	J3QTR3
G	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	151	32% helix, 17% strand	P61088

Pockets

3 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	990	0.79	0.81	87	empty
2	917	0.75	0.78	93	empty
3	114	0.45	0.78	28	empty

Interfaces

3 interfaces between chains.

B–C · 1389 Å² buried · 20 hydrogen bonds · protein-protein
B–G · 1235 Å² buried · 10 hydrogen bonds · protein-protein
C–G · 178 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6KG6 · Crystal structure of MavC/UBE2N-Ub complex · the same entry in another collection · chain B against B, 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 G 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 J3QTR3
Every structure of UniProt P61088
Elsewhere: RCSB PDB 6KG6 · PDBe 6KG6 · UniProt A0A2S6F4I5 · UniProt J3QTR3 · UniProt P61088

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