MolNFT v1 · #9099 · protein

The structure of holo type human cu, zn superoxide dismutase

1HL5: “The structure of holo type human cu, zn superoxide dismutase”. X-ray diffraction, 3 ligands (CU, ZN, CA), 20 pockets (best druggability 0.76). MolNFT v1 #9099 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1HL5
Type: protein
Length: 2,738 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase
EC: 1.15.1.1
UniProt: P00441
Ligands: CU, ZN, CA
Pockets: 20 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, G, H, I, J, K, N, O, Q, S	Superoxide dismutase (EC 1.15.1.1)	protein	153	6% helix, 41% strand	P00441
E	Superoxide dismutase (EC 1.15.1.1)	protein	151	6% helix, 42% strand	P00441
F	Superoxide dismutase (EC 1.15.1.1)	protein	144	6% helix, 39% strand	P00441
L	Superoxide dismutase (EC 1.15.1.1)	protein	152	6% helix, 40% strand	P00441
M	Superoxide dismutase (EC 1.15.1.1)	protein	150	5% helix, 40% strand	P00441
P	Superoxide dismutase (EC 1.15.1.1)	protein	152	6% helix, 41% strand	P00441

Ligands and binding sites

CU · Copper (II) ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, S
ZN · Zinc ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, S
CA · Calcium ion · metal · 3 copies · chains C, D, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1109	0.76	0.78	123	empty
2	873	0.75	0.79	91	empty
3	1074	0.74	0.77	109	empty
4	680	0.71	0.78	67	empty
5	708	0.71	0.78	95	empty

Interfaces

36 interfaces between chains.

F–M · 722 Å² buried · 4 hydrogen bonds · protein-protein
D–K · 721 Å² buried · 4 hydrogen bonds · protein-protein
P–S · 719 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 719 Å² buried · 4 hydrogen bonds · protein-protein
B–I · 716 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

1HL5 · The Structure of Holo Type Human Cu, Zn Superoxide Dismutase · 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 1HL5 · PDBe 1HL5 · UniProt P00441

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