Research workbench
Crystal structure of a dyp-type peroxidase from pseudomonas putida
Analyse Crystal structure of a dyp-type peroxidase from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QYQ
- Type
- protein
- Length
- 1,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp-type peroxidase family protein
- UniProt
- Q88HV5
- Ligands
- HEM
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dyp-type peroxidase family protein | protein | 283 | 27% helix, 27% strand | Q88HV5 |
| B | Dyp-type peroxidase family protein | protein | 284 | 27% helix, 27% strand | Q88HV5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.82 | 0.92 | 34 | HEM |
| 2 | 293 | 0.82 | 0.92 | 34 | HEM |
| 3 | 304 | 0.81 | 0.91 | 34 | HEM |
| 4 | 428 | 0.80 | 0.88 | 56 | HEM |
| 5 | 684 | 0.74 | 0.80 | 79 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1211 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1210 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 899 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7QYQ · Crystal structure of a DyP-type peroxidase from Pseudomonas putida · 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 Q88HV5
- Elsewhere: RCSB PDB 7QYQ · PDBe 7QYQ · UniProt Q88HV5
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