MolNFT v1 · #95298 · protein
Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin a from amphitrite ornata
4ILZ · Dehaloperoxidase a: “Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin a from…”. X-ray diffraction, 4 ligands (HEM, TBP, SO4), 3 pockets (best druggability 0.71). MolNFT v1 #95298 on…
- PDB
- 4ILZ
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase a
- UniProt
- Q9NAV8
- Ligands
- HEM, TBP, SO4, OXY
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase a | protein | 137 | 75% helix, 1% strand | Q9NAV8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TBP · 2,4,6-tribromophenol · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- OXY · Oxygen molecule · ion · chains A
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B
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 | 212 | 0.71 | 0.87 | 23 | HEM, TBP, OXY |
| 2 | 239 | 0.71 | 0.86 | 26 | HEM |
| 3 | 101 | 0.36 | 0.74 | 21 | IPA |
Interfaces
1 interface between chains.
- A–B · 237 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ILZ · Structural and kinetic study of an internal substrate binding site of… · 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 Q9NAV8
- Elsewhere: RCSB PDB 4ILZ · PDBe 4ILZ · UniProt Q9NAV8
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