MolNFT v1 · #184228 · protein

Mouse RNF213, with mixed nucleotides bound

7OIM · E3 ubiquitin-protein ligase RNF213: “Mouse RNF213, with mixed nucleotides bound”. Electron microscopy, 5 ligands (ATP, ADP, AGS), 20 pockets (best druggability 0.86). MolNFT v1 #184228 on GenesisL1: 3D structure, binding sites and…

PDB: 7OIM
Type: protein
Length: 4,426 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RNF213
EC: 2.3.2.27, 3.6.4.-
UniProt: E9Q555
Ligands: ATP, ADP, AGS, ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 52% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF213 (EC 2.3.2.27, 3.6.4.-)	protein	4426	52% helix, 5% strand	E9Q555

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains A
AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.86	0.87	140	empty
2	1031	0.83	0.84	100	AGS
3	1070	0.82	0.83	100	empty
4	1128	0.79	0.80	92	empty
5	976	0.79	0.81	75	ATP, MG

Modifications

Observed in the structure: 2 disulfide (disulfide).

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 E9Q555
Elsewhere: RCSB PDB 7OIM · PDBe 7OIM · UniProt E9Q555

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