MolNFT v1 · #141020 · protein

Structure of human SOD1 complexed with isoproteranol in C2221 space group

5YTU · Superoxide dismutase [cu-zn]: “Structure of human SOD1 complexed with isoproteranol in C2221 space group”. X-ray diffraction, 4 ligands (S4P, 5FW, TAM), 16 pockets (best druggability 0.81). MolNFT v1 #141020 on GenesisL1: 3D…

PDB: 5YTU
Type: protein
Length: 1,508 residues
Chains: 10
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: S4P, 5FW, TAM, ZN
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H, B, C, D, F	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	154	8% helix, 39% strand	P00441
E	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	155	6% helix, 39% strand	P00441
G	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	125	6% helix, 49% strand	P00441
I, J	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	152	8% helix, 40% strand	P00441

Ligands and binding sites

S4P · Dihydrogen tetrasulfide · ligand · 3 copies · chains A, H, B, C, D, E
5FW · Isoprenaline · ligand · chains A
TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
ZN · Zinc ion · metal · 9 copies · chains A, H, B, C, D, E, F, I, J
GOL · Glycerol · additive · 2 copies · chains H, B, G

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	965	0.81	0.83	116	S4P
2	147	0.67	0.88	32	empty
3	264	0.66	0.83	43	empty
4	181	0.65	0.85	34	empty
5	332	0.63	0.79	46	GOL

Interfaces

13 interfaces between chains.

A–H · 805 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 782 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 746 Å² buried · 5 hydrogen bonds · protein-protein
I–J · 737 Å² buried · 4 hydrogen bonds · protein-protein
F–G · 730 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

5YTU · Structure of human SOD1 complexed with isoproteranol in C2221 space group · 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 5YTU · PDBe 5YTU · UniProt P00441

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