MolNFT v1 · #167137 · protein
The C2 crystal form of sodci superoxide dismutase at 1.7 a resolution with 6 molecules in the asymmetric unit.
6VBS · Superoxide dismutase [cu-zn]: “The C2 crystal form of sodci superoxide dismutase at 1.7 a resolution with 6 molecules in the asymmetric unit.”. X-ray diffraction, 3 ligands (CU, ZN, SO4), 4 pockets (best druggability 0.79). MolNFT…
- PDB
- 6VBS
- Type
- protein
- Length
- 934 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
- A0A0D6GQL3
- Ligands
- CU, ZN, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 156 | 7% helix, 40% strand | A0A0D6GQL3 |
| B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 155 | 7% helix, 42% strand | A0A0D6GQL3 |
| C | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 156 | 6% helix, 42% strand | A0A0D6GQL3 |
| D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 159 | 6% helix, 41% strand | A0A0D6GQL3 |
| F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 152 | 7% helix, 39% strand | A0A0D6GQL3 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.79 | 0.81 | 120 | SO4 |
| 2 | 126 | 0.41 | 0.75 | 28 | empty |
| 3 | 61 | 0.35 | 0.78 | 19 | empty |
| 4 | 65 | 0.28 | 0.73 | 16 | SO4 |
Interfaces
8 interfaces between chains.
- B–D · 765 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 749 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 749 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 630 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 367 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6VBS · The C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolution with 6 molecules in… · 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 A0A0D6GQL3
- Elsewhere: RCSB PDB 6VBS · PDBe 6VBS · UniProt A0A0D6GQL3
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