Research workbench
Crystal structure of holo-type bacterial vanadium-dependent chloroperoxidase
Analyse Crystal structure of holo-type bacterial vanadium-dependent chloroperoxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W36
- Type
- protein
- Length
- 941 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAPH1
- EC
- 1.11.1.10
- UniProt
- A7KH27
- Ligands
- VO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAPH1 (EC 1.11.1.10) | protein | 470 | 49% helix, 7% strand | A7KH27 |
| B | NAPH1 (EC 1.11.1.10) | protein | 471 | 50% helix, 8% strand | A7KH27 |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.80 | 0.86 | 42 | empty |
| 2 | 493 | 0.79 | 0.86 | 44 | empty |
| 3 | 936 | 0.76 | 0.79 | 74 | empty |
| 4 | 842 | 0.74 | 0.79 | 74 | empty |
| 5 | 74 | 0.74 | 0.98 | 25 | VO4 |
Interfaces
1 interface between chains.
- A–B · 2106 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3W36 · Crystal structure of holo-type bacterial Vanadium-dependent chloroperoxidase · 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 A7KH27
- Elsewhere: RCSB PDB 3W36 · PDBe 3W36 · UniProt A7KH27
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