Research workbench
Crystal structure of a dyp-type peroxidase from bacillus subtilis in P3121 space group
Analyse Crystal structure of a dyp-type peroxidase from bacillus subtilis in P3121… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PKX
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE
- EC
- 1.11.1.-
- UniProt
- A0A162R372
- Ligands
- HEM
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 354 | 26% helix, 23% strand | A0A162R372 |
| B | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 353 | 27% helix, 23% strand | A0A162R372 |
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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.82 | 0.90 | 49 | HEM |
| 2 | 430 | 0.82 | 0.89 | 50 | HEM |
| 3 | 405 | 0.66 | 0.79 | 54 | empty |
| 4 | 205 | 0.61 | 0.82 | 29 | empty |
| 5 | 321 | 0.57 | 0.76 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 2324 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 7PKX · Crystal structure of a DyP-type peroxidase from Bacillus subtilis in P3121 space group · 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 A0A162R372
- Elsewhere: RCSB PDB 7PKX · PDBe 7PKX · UniProt A0A162R372
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