MolNFT v1 · #107785 · protein
Pikc D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group
4UMZ · Cytochrome P450 hydroxylase pikc: “Pikc D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group”. X-ray diffraction, 2 ligands (HEM, XJO), 5 pockets (best druggability 0.85). MolNFT…
- PDB
- 4UMZ
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 hydroxylase pikc
- UniProt
- O87605
- Ligands
- HEM, XJO
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 hydroxylase pikc | protein | 396 | 53% helix, 10% strand | O87605 |
| B | Cytochrome P450 hydroxylase pikc | protein | 395 | 53% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- XJO · (3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 2-[(dimethylamino)methyl]benzoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.85 | 0.86 | 80 | HEM, XJO |
| 2 | 1051 | 0.85 | 0.85 | 78 | HEM, XJO |
| 3 | 814 | 0.74 | 0.79 | 61 | empty |
| 4 | 166 | 0.46 | 0.76 | 25 | empty |
| 5 | 55 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4UMZ · PikC D50N mutant in complex with the engineered substrate mimic bearing a… · 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 4UMZ · PDBe 4UMZ · UniProt O87605
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