Research workbench
FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase
Analyse FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MAB
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.436
- Source
- Rhodobacter sp. SW2
- Molecule
- FoxE
- UniProt
- A3DTD8
- Ligands
- HEC, CU, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.436 · 2 distinct chains · 41% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FoxE | protein | 259 | 41% helix, 3% strand | A3DTD8 |
| C | FoxE | protein | 257 | 41% helix, 4% strand | A3DTD8 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, B, C
- CU · Copper (II) ion · metal · chains B
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.76 | 0.83 | 57 | HEC |
| 2 | 468 | 0.76 | 0.84 | 58 | HEC |
| 3 | 478 | 0.75 | 0.83 | 50 | HEC |
| 4 | 303 | 0.73 | 0.86 | 35 | HEC, PO4 |
| 5 | 344 | 0.71 | 0.84 | 35 | HEC, PO4 |
Interfaces
3 interfaces between chains.
- A–B · 1056 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1054 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1037 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 3 disulfide (heme c attachment, disulfide).
Compared structures
- 5MAB · Foxe P3121 crystal structure of rhodopseudomonas ferrooxidans SW2 putative iron oxidase · 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 A3DTD8
- Elsewhere: RCSB PDB 5MAB · PDBe 5MAB · UniProt A3DTD8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.