Research workbench
Crystal structure of E.COLI iron superoxide dismutase Q69E at 1.1 ångström resolution
Analyse Crystal structure of E.COLI iron superoxide dismutase Q69E at 1.1 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NYB
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [fe]
- EC
- 1.15.1.1
- UniProt
- P0AGD3
- Ligands
- FE2, O
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase [fe] (EC 1.15.1.1) | protein | 192 | 52% helix, 12% strand | P0AGD3 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- O · Oxygen atom · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.83 | 0.85 | 77 | empty |
| 2 | 209 | 0.58 | 0.80 | 19 | empty |
| 3 | 191 | 0.55 | 0.79 | 21 | empty |
| 4 | 154 | 0.52 | 0.79 | 27 | empty |
| 5 | 91 | 0.43 | 0.79 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 987 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 209 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2NYB · Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGD3 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P0AGD3) · a predicted model of the same protein · 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 P0AGD3
- Elsewhere: RCSB PDB 2NYB · PDBe 2NYB · UniProt P0AGD3
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