MolNFT v1 · #167186 · protein
Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III) mesoporphyrin IX and substrate trichlorophenol
6VD5: “Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III) mesoporphyrin IX and substrate…”. X-ray diffraction, 3 ligands (MH0, T6C, SO4), 2 pockets (best druggability 0.64). MolNFT v1 #167186 on GenesisL1: 3D…
- PDB
- 6VD5
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- MH0, T6C, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehaloperoxidase B | protein | 133 | 71% helix, 2% strand | Q9NAV7 |
| B | Dehaloperoxidase B | protein | 132 | 73% helix, 2% strand | Q9NAV7 |
Ligands and binding sites
- MH0 · Mesoheme · ligand · 2 copies · chains A, B
- T6C · 2,4,6-trichlorophenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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 | 294 | 0.64 | 0.80 | 28 | MH0, T6C |
| 2 | 271 | 0.62 | 0.79 | 24 | T6C, MH0 |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6VD5 · Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin… · 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 6VD5 · PDBe 6VD5 · UniProt Q9NAV7
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