MolNFT v1 · #52394 · protein
Crystal structure of the narbomycin-bound pikc D50N mutant
2VZM · Cytochrome P450 monooxygenase: “Crystal structure of the narbomycin-bound pikc D50N mutant”. X-ray diffraction, 2 ligands (HEM, NRB), 4 pockets (best druggability 0.86). MolNFT v1 #52394 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VZM
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- O87605
- Ligands
- HEM, NRB
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 monooxygenase | protein | 395 | 52% helix, 10% strand | O87605 |
| B | Cytochrome P450 monooxygenase | protein | 394 | 53% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NRB · Narbomycin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.86 | 0.87 | 80 | HEM, NRB |
| 2 | 1068 | 0.85 | 0.86 | 79 | HEM, NRB |
| 3 | 845 | 0.74 | 0.79 | 66 | empty |
| 4 | 119 | 0.41 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VZM · Crystal structure of the narbomycin-bound PikC D50N mutant · the same entry in another collection · chain A against A, TM-score 1.00
- O87605 · AlphaFold monomer V2.0 prediction for cytochrome P450 monooxygenase pikc (O87605) · a predicted model of the same protein · chain B 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 O87605
- Elsewhere: RCSB PDB 2VZM · PDBe 2VZM · UniProt O87605
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