MolNFT v1 · #28177 · protein
Crystal structure of manganese superoxide dismutase from deinococcus radiodurans
1Y67: “Crystal structure of manganese superoxide dismutase from deinococcus radiodurans”. X-ray diffraction, 1 ligand (FE), 9 pockets (best druggability 0.75). MolNFT v1 #28177 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1Y67
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- Q9RUV2
- Ligands
- FE
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 210 | 51% helix, 12% strand | Q9RUV2 |
| B | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 204 | 50% helix, 12% strand | Q9RUV2 |
| C | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 204 | 53% helix, 12% strand | Q9RUV2 |
| D | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 214 | 51% helix, 13% strand | Q9RUV2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.75 | 0.81 | 63 | empty |
| 2 | 186 | 0.54 | 0.79 | 19 | empty |
| 3 | 183 | 0.54 | 0.79 | 20 | empty |
| 4 | 169 | 0.53 | 0.79 | 19 | empty |
| 5 | 174 | 0.52 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 954 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1Y67 · Crystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans · the same entry in another collection · chain D against D, TM-score 1.00
- Q9RUV2 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn] (Q9RUV2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9RUV2
- Elsewhere: RCSB PDB 1Y67 · PDBe 1Y67 · UniProt Q9RUV2
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