MolNFT v1 · #164172 · protein
A4V mutant of human superoxide dismutase 1 with ebselen bond in C2 space group
6SPH · Superoxide dismutase [cu-zn]: “A4V mutant of human superoxide dismutase 1 with ebselen bond in C2 space group”. X-ray diffraction, 3 ligands (9JT, ZN, SO4), 7 pockets (best druggability 0.78). MolNFT v1 #164172 on GenesisL1: 3D…
- PDB
- 6SPH
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- 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
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, J, L | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 41% strand | P00441 |
Ligands and binding sites
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 6 copies · chains A, C, E, G, J, L
- ZN · Zinc ion · metal · 6 copies · chains A, C, E, G, J, L
- SO4 · Sulfate ion · ion · 3 copies · chains A, G, C, J
- GOL · Glycerol · additive · 7 copies · chains A, C, G, J, L
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains E, G, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.78 | 0.80 | 101 | SO4 |
| 2 | 176 | 0.66 | 0.86 | 34 | GOL |
| 3 | 222 | 0.66 | 0.84 | 42 | empty |
| 4 | 208 | 0.65 | 0.84 | 36 | empty |
| 5 | 69 | 0.30 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- E–G · 759 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 747 Ų buried · 5 hydrogen bonds · protein-protein
- J–L · 736 Ų buried · 5 hydrogen bonds · protein-protein
- G–J · 440 Ų buried · 6 hydrogen bonds · protein-protein
- C–J · 352 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 disulfide (covalent ligand, disulfide).
Compared structures
- 6SPH · A4V mutant of human superoxide dismutase 1 with ebselen bond in C2 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 6SPH · PDBe 6SPH · UniProt P00441
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