Research workbench
X-ray siras structure determination of a vanadium-dependent haloperoxidase from ascophyllum nodosum at 2.0 a resolution
Analyse X-ray siras structure determination of a vanadium-dependent haloperoxidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QI9
- Type
- protein
- Length
- 1,111 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (vanadium bromoperoxidase)
- EC
- 1.11.1.10
- UniProt
- P81701
- Ligands
- IOD, VO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (vanadium bromoperoxidase) (EC 1.11.1.10) | protein | 555 | 45% helix, 9% strand | P81701 |
| B | Protein (vanadium bromoperoxidase) (EC 1.11.1.10) | protein | 556 | 44% helix, 8% strand | P81701 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.78 | 0.88 | 74 | empty |
| 2 | 447 | 0.74 | 0.83 | 67 | VO4 |
| 3 | 430 | 0.73 | 0.83 | 56 | VO4 |
| 4 | 59 | 0.53 | 0.87 | 26 | empty |
| 5 | 213 | 0.52 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 5484 Ų buried · 107 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1QI9 · X-ray siras structure determination of a vanadium-dependent haloperoxidase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P81701 · AlphaFold monomer V2.0 prediction for vanadium-dependent bromoperoxidase (P81701) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P81701
- Elsewhere: RCSB PDB 1QI9 · PDBe 1QI9 · UniProt P81701
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