MolNFT v1 · #186108 · protein
Crystal structure of a dyp-type peroxidase 29E4 variant from pseudomonas putida
7QZA · Dyp-type peroxidase family protein: “Crystal structure of a dyp-type peroxidase 29E4 variant from pseudomonas putida”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.84). MolNFT v1 #186108 on GenesisL1: 3D…
- PDB
- 7QZA
- Type
- protein
- Length
- 2,264 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp-type peroxidase family protein
- UniProt
- Q88HV5
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Dyp-type peroxidase family protein | protein | 283 | 26% helix, 29% strand | Q88HV5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.84 | 0.95 | 34 | HEM |
| 2 | 282 | 0.82 | 0.93 | 35 | HEM |
| 3 | 280 | 0.82 | 0.93 | 35 | HEM |
| 4 | 278 | 0.82 | 0.93 | 38 | HEM |
| 5 | 280 | 0.82 | 0.93 | 34 | HEM |
Interfaces
14 interfaces between chains.
- C–G · 1263 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1093 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 944 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 933 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 911 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme attachment).
Compared structures
- 7QZA · Crystal structure of a DyP-type peroxidase 29E4 variant 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 7QZA · PDBe 7QZA · UniProt Q88HV5
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