MolNFT v1 · #172123 · protein
Chaetomium thermophilum cuzn-superoxide dismutase
6ZS1 · Superoxide dismutase [cu-zn]: “Chaetomium thermophilum cuzn-superoxide dismutase”. X-ray diffraction, 4 ligands (NA, ZN, CU), 9 pockets (best druggability 0.81). MolNFT v1 #172123 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZS1
- Type
- protein
- Length
- 1,239 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- G0S1F8
- Ligands
- NA, ZN, CU, PO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 157 | 6% helix, 37% strand | G0S1F8 |
| C, D, E, F, G | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 6% helix, 37% strand | G0S1F8 |
| H | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 155 | 6% helix, 37% strand | G0S1F8 |
Ligands and binding sites
- NA · Sodium ion · metal · 15 copies · chains A, D, B, C, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CU · Copper (II) ion · metal · 4 copies · chains C, D, E, F
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, G, C, D, H
- GOL · Glycerol · additive · 4 copies · chains C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.81 | 0.91 | 44 | NA |
| 2 | 816 | 0.80 | 0.83 | 98 | PO4, NA |
| 3 | 762 | 0.80 | 0.84 | 80 | NA |
| 4 | 309 | 0.80 | 0.90 | 37 | empty |
| 5 | 116 | 0.66 | 0.89 | 24 | empty |
Interfaces
16 interfaces between chains.
- B–E · 746 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 743 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 509 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 487 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ZS1 · Chaetomium thermophilum CuZn-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 G0S1F8
- Elsewhere: RCSB PDB 6ZS1 · PDBe 6ZS1 · UniProt G0S1F8
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