MolNFT v1 · #191271 · protein
Structure of NAPH3, a vanadium-dependent haloperoxidase homolog catalyzing the stereospecific alpha-hydroxyketone rearrangement reaction in napyradiomycin biosynthesis
8CXL: “Structure of NAPH3, a vanadium-dependent haloperoxidase homolog catalyzing the stereospecific…”. X-ray diffraction, 2 ligands (MG, CL), 5 pockets (best druggability 0.78). MolNFT v1 #191271 on GenesisL1: 3D structure, binding sites…
- PDB
- 8CXL
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAPH3
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAPH3 | protein | 472 | 48% helix, 8% strand | — |
| B | NAPH3 | protein | 464 | 49% helix, 9% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.78 | 0.81 | 93 | empty |
| 2 | 442 | 0.76 | 0.84 | 59 | empty |
| 3 | 711 | 0.74 | 0.80 | 75 | empty |
| 4 | 76 | 0.72 | 0.97 | 27 | empty |
| 5 | 410 | 0.71 | 0.82 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 2213 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 8CXL · Structure of NapH3, a vanadium-dependent haloperoxidase homolog catalyzing the… · 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
- Elsewhere: RCSB PDB 8CXL · PDBe 8CXL
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