MolNFT v1 · #178884 · protein
Neutron structure of ferric dehaloperoxidase B
7JOR: “Neutron structure of ferric dehaloperoxidase B”. Neutron diffraction, 1 ligand (HEM), 3 pockets (best druggability 0.76). MolNFT v1 #178884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JOR
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- neutron diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- HEM
- Pockets
- 3 · best druggability 0.76
Structure
neutron diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 76% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.76 | 0.87 | 26 | HEM, PG0 |
| 2 | 280 | 0.65 | 0.81 | 38 | HEM |
| 3 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7JOR · Neutron structure of ferric Dehaloperoxidase B · 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 Q9NAV7
- Elsewhere: RCSB PDB 7JOR · PDBe 7JOR · UniProt Q9NAV7
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