MolNFT v1 · #128888 · protein

SOD1 bound to ebselen

5O40 · Superoxide dismutase [cu-zn]: “SOD1 bound to ebselen”. X-ray diffraction, 3 ligands (9JT, ZN, SO4), 2 pockets (best druggability 0.61). MolNFT v1 #128888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O40
Type: protein
Length: 306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [cu-zn]
EC: 1.15.1.1
UniProt: P00441
Ligands: 9JT, ZN, SO4
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	153	5% helix, 41% strand	P00441

Ligands and binding sites

9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 2 copies · chains A, F
ZN · Zinc ion · metal · 4 copies · chains A, F
SO4 · Sulfate ion · ion · 2 copies · chains A, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.61	0.82	26	empty
2	87	0.32	0.73	19	9JT

Interfaces

1 interface between chains.

A–F · 682 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5O40 · SOD1 bound to Ebselen · the same entry in another collection · chain A against A, TM-score 1.00

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 P00441
Elsewhere: RCSB PDB 5O40 · PDBe 5O40 · UniProt P00441

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