MolNFT v1 · #164173 · protein

A4V mutant of human SOD1 with ebselen derivative 4

6SPI · Superoxide dismutase [cu-zn]: “A4V mutant of human SOD1 with ebselen derivative 4”. X-ray diffraction, 3 ligands (LQW, ZN, SO4), 14 pockets (best druggability 0.78). MolNFT v1 #164173 on GenesisL1: 3D structure, binding sites and…

PDB: 6SPI
Type: protein
Length: 1,836 residues
Chains: 12
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: LQW, ZN, SO4
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	153	6% helix, 41% strand	P00441

Ligands and binding sites

LQW · ~{N}-[(4-chlorophenyl)methyl]-2-selanyl-benzamide · ligand · 12 copies · chains A, B, K, C, I, D, L, E, G, F, H, J
ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, F, E, G, H, J, K, L

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

Pockets

14 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	1041	0.78	0.80	108	SO4
2	821	0.71	0.77	112	empty
3	586	0.70	0.79	103	empty
4	739	0.69	0.77	66	SO4
5	638	0.68	0.77	80	empty

Interfaces

21 interfaces between chains.

A–J · 773 Å² buried · 7 hydrogen bonds · protein-protein
B–K · 768 Å² buried · 5 hydrogen bonds · protein-protein
D–L · 753 Å² buried · 5 hydrogen bonds · protein-protein
C–I · 748 Å² buried · 6 hydrogen bonds · protein-protein
E–G · 738 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent, 12 disulfide (covalent ligand, disulfide).

Compared structures

6SPI · A4V mutant of human SOD1 with ebselen derivative 4 · 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 6SPI · PDBe 6SPI · UniProt P00441

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.