MolNFT v1 · #176177 · protein
Crystal structure of a mutant staphylococcus equorum manganese superoxide dismutase S126C
7DDW: “Crystal structure of a mutant staphylococcus equorum manganese superoxide dismutase S126C”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.80). MolNFT v1 #176177 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DDW
- Type
- protein
- Length
- 1,187 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- A0A1E5TT85
- Ligands
- MN
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Superoxide dismutase (EC 1.15.1.1) | protein | 198 | 55% helix, 13% strand | A0A1E5TT85 |
| B | Superoxide dismutase (EC 1.15.1.1) | protein | 197 | 57% helix, 13% strand | A0A1E5TT85 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.80 | 0.82 | 130 | empty |
| 2 | 511 | 0.74 | 0.83 | 90 | empty |
| 3 | 461 | 0.72 | 0.82 | 65 | empty |
| 4 | 283 | 0.65 | 0.81 | 36 | empty |
| 5 | 223 | 0.64 | 0.83 | 26 | empty |
Interfaces
12 interfaces between chains.
- C–D · 934 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 923 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 386 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 371 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7DDW · Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase S126C · 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 A0A1E5TT85
- Elsewhere: RCSB PDB 7DDW · PDBe 7DDW · UniProt A0A1E5TT85
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