Research workbench
Sfx structure of damage free ferric state of dye type peroxidase aa from streptomyces lividans
Analyse Sfx structure of damage free ferric state of dye type peroxidase aa from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I43
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE
- EC
- 1.11.1.-
- UniProt
- Q9RKQ2
- Ligands
- HEM
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 362 | 27% helix, 20% strand | Q9RKQ2 |
| B | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 362 | 28% helix, 21% strand | Q9RKQ2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.83 | 0.87 | 72 | HEM |
| 2 | 331 | 0.82 | 0.92 | 44 | HEM |
| 3 | 91 | 0.59 | 0.87 | 15 | empty |
| 4 | 138 | 0.57 | 0.82 | 24 | empty |
| 5 | 247 | 0.56 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2314 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6I43 · SFX Structure of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces… · 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 Q9RKQ2
- Elsewhere: RCSB PDB 6I43 · PDBe 6I43 · UniProt Q9RKQ2
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