MolNFT v1 · #156401 · protein
Crystal structure of a mutant staphylococcus equorum manganese superoxide dismutase N73F
6M30: “Crystal structure of a mutant staphylococcus equorum manganese superoxide dismutase N73F”. X-ray diffraction, 1 ligand (MN), 14 pockets (best druggability 0.74). MolNFT v1 #156401 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6M30
- Type
- protein
- Length
- 1,188 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
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Superoxide dismutase (EC 1.15.1.1) | protein | 198 | 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.74 | 0.78 | 84 | empty |
| 2 | 533 | 0.73 | 0.81 | 55 | empty |
| 3 | 696 | 0.73 | 0.79 | 58 | empty |
| 4 | 474 | 0.68 | 0.79 | 66 | empty |
| 5 | 437 | 0.66 | 0.78 | 42 | empty |
Interfaces
12 interfaces between chains.
- C–D · 949 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 946 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 942 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 464 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6M30 · Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F · 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 6M30 · PDBe 6M30 · UniProt A0A1E5TT85
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