MolNFT v1 · #161091 · protein
Dye type peroxidase aa from streptomyces lividans: 235.2 kgy structure
6Q3D · DEFERROCHELATASE/PEROXIDASE: “Dye type peroxidase aa from streptomyces lividans: 235.2 kgy structure”. X-ray diffraction, 1 ligand (HEM), 9 pockets (best druggability 0.83). MolNFT v1 #161091 on GenesisL1: 3D structure, binding…
- PDB
- 6Q3D
- Type
- protein
- Length
- 723 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, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 362 | 27% helix, 22% strand | Q9RKQ2 |
| B | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 361 | 27% 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 | 786 | 0.83 | 0.86 | 80 | HEM |
| 2 | 373 | 0.82 | 0.91 | 50 | HEM |
| 3 | 129 | 0.60 | 0.85 | 32 | empty |
| 4 | 274 | 0.58 | 0.78 | 30 | empty |
| 5 | 83 | 0.57 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2329 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6Q3D · Dye type peroxidase Aa from Streptomyces lividans: 235.2 kGy structure · 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 6Q3D · PDBe 6Q3D · UniProt Q9RKQ2
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