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Hoip-HOIPIN8 complex

Analyse Hoip-HOIPIN8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KC6
Type: protein
Length: 1,184 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RNF31
EC: 2.3.2.31
UniProt: Q96EP0
Ligands: D60, ZN, CL
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, K	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	197	29% helix, 10% strand	Q96EP0
C, E	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	198	29% helix, 10% strand	Q96EP0
G	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	197	29% helix, 10% strand	Q96EP0

Ligands and binding sites

D60 · 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl) benzoic acid · ligand · 6 copies · chains A, I, C, K, E, G
ZN · Zinc ion · metal · 24 copies · chains A, C, E, G, I, K
CL · Chloride ion · ion · 9 copies · chains A, C, E, G, I, K
GOL · Glycerol · additive · 10 copies · chains A, C, K, E, G

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

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	628	0.77	0.83	64	CL
2	622	0.75	0.81	55	GOL, CL
3	675	0.74	0.80	94	empty
4	392	0.72	0.83	42	D60, GOL
5	243	0.66	0.83	39	GOL

Interfaces

5 interfaces between chains.

C–K · 783 Å² buried · 7 hydrogen bonds · protein-protein
A–I · 721 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 683 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 676 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 567 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

6KC6 · HOIP-HOIPIN8 complex · the same entry in another collection · chain K against K, 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 A against A, TM-score 0.93

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 6KC6 · PDBe 6KC6 · UniProt Q96EP0

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