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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Foxe
- UniProt
- A3DTD8
- Ligands
- HEC, CU, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 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
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