MolNFT v1 · #150642 · protein

Hoip-FRAGMENT5 complex

6GZY · E3 ubiquitin-protein ligase RNF31: “Hoip-FRAGMENT5 complex”. X-ray diffraction, 4 ligands (FHH, ZN, NA), 6 pockets (best druggability 0.68). MolNFT v1 #150642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GZY
Type: protein
Length: 393 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RNF31
EC: 2.3.2.27
UniProt: Q96EP0
Ligands: FHH, ZN, NA, SO4
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.27)	protein	199	33% helix, 9% strand	Q96EP0
B	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.27)	protein	194	32% helix, 11% strand	Q96EP0

Ligands and binding sites

FHH · Methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl) carbonylamino]butanoate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 8 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
PGE · Triethylene glycol · additive · chains A

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

Pockets

6 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	56	0.68	0.96	18	EDO
2	534	0.63	0.75	63	FHH, SO4, NA
3	451	0.62	0.76	38	SO4, FHH
4	186	0.45	0.74	24	SO4, NA
5	74	0.42	0.80	12	EDO

Interfaces

1 interface between chains.

A–B · 528 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6GZY · HOIP-fragment5 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · 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 Q96EP0
Elsewhere: RCSB PDB 6GZY · PDBe 6GZY · UniProt Q96EP0

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