MolNFT v1 · #167208 · protein
Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III) deuteroporphyrin IX and substrate 4-bromophenol
6VDR: “Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III) deuteroporphyrin IX and substrate…”. X-ray diffraction, 3 ligands (FDE, BML, SO4), 2 pockets (best druggability 0.66). MolNFT v1 #167208 on GenesisL1: 3D…
- PDB
- 6VDR
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- FDE, BML, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 72% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- FDE · Fe(iii) deuteroporphyrin IX · ligand · 2 copies · chains A, B
- BML · 4-bromophenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.66 | 0.82 | 30 | FDE, BML |
| 2 | 312 | 0.66 | 0.81 | 33 | FDE, BML |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VDR · Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III)… · 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 6VDR · PDBe 6VDR · UniProt Q9NAV7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.