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Crystal structure of Sphingomonas sp. A1 peroxidase EfeB responsible for import of iron
Analyse Crystal structure of Sphingomonas sp. A1 peroxidase EfeB responsible for import… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JBN
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Sphingomonas sp. A1
- Molecule
- Peroxidase EfeB
- Ligands
- HEM, OXY
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxidase EfeB | protein | 391 | 27% helix, 23% strand | — |
| B | Peroxidase EfeB | protein | 390 | 27% helix, 23% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.84 | 0.94 | 44 | HEM, OXY |
| 2 | 308 | 0.83 | 0.93 | 46 | HEM, OXY |
| 3 | 426 | 0.70 | 0.81 | 58 | PEG, EDO, PGE |
| 4 | 411 | 0.66 | 0.79 | 60 | EDO, PEG |
| 5 | 127 | 0.45 | 0.77 | 27 | EDO |
Interfaces
1 interface between chains.
- A–B · 3735 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6JBN · Crystal structure of sphingomonas sp. A1 peroxidase efeb responsible for import of iron · 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
- Elsewhere: RCSB PDB 6JBN · PDBe 6JBN
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