MolNFT v1 · #86460 · protein
Pikc bound to the 10-dml analog with the 3-(N,N-dimethylamino) propanoate anchoring group
4B7D · Cytochrome P450 hydroxylase pikc: “Pikc bound to the 10-dml analog with the 3-(N,N-dimethylamino) propanoate anchoring group”. X-ray diffraction, 2 ligands (HEM, QLE), 4 pockets (best druggability 0.87). MolNFT v1 #86460 on…
- PDB
- 4B7D
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 hydroxylase pikc
- UniProt
- O87605
- Ligands
- HEM, QLE
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 hydroxylase pikc | protein | 393 | 55% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- QLE · [(3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-bis(oxidanylidene)-1-oxacyclododec-9-en-4-yl] 3-(dimethylamino)propanoate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.87 | 0.88 | 75 | GOL, HEM, QLE |
| 2 | 969 | 0.86 | 0.87 | 76 | GOL, HEM, QLE |
| 3 | 294 | 0.49 | 0.73 | 26 | empty |
| 4 | 190 | 0.48 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B7D · PikC bound to the 10-DML analog with the 3-(N,N-dimethylamino) propanoate anchoring group · 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 A 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 4B7D · PDBe 4B7D · UniProt O87605
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