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Homohexameric structure of the second vanadate-dependent bromoperoxidase (anii) from ascophyllum nodosum
Analyse Homohexameric structure of the second vanadate-dependent bromoperoxidase (anii)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AA6
- Type
- protein
- Length
- 3,565 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanadium-dependent bromoperoxidase 2
- EC
- 1.11.1.18
- UniProt
- K7ZUA3
- Ligands
- VO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Vanadium-dependent bromoperoxidase 2 (EC 1.11.1.18) | protein | 594 | 41% helix, 10% strand | K7ZUA3 |
| B | Vanadium-dependent bromoperoxidase 2 (EC 1.11.1.18) | protein | 595 | 41% helix, 11% strand | K7ZUA3 |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.85 | 0.97 | 43 | empty |
| 2 | 270 | 0.85 | 0.97 | 42 | empty |
| 3 | 254 | 0.84 | 0.96 | 41 | empty |
| 4 | 572 | 0.72 | 0.80 | 60 | VO4 |
| 5 | 575 | 0.71 | 0.80 | 51 | VO4 |
Interfaces
12 interfaces between chains.
- D–E · 6482 Ų buried · 125 hydrogen bonds · protein-protein
- B–C · 6473 Ų buried · 127 hydrogen bonds · protein-protein
- A–F · 6441 Ų buried · 126 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 660 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5AA6 · Homohexameric Structure of the second Vanadate-Dependent Bromoperoxidase (AnII) from… · 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 K7ZUA3
- Elsewhere: RCSB PDB 5AA6 · PDBe 5AA6 · UniProt K7ZUA3
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