Research workbench
Pikc D50N mutant bound to the 10-dml analog with the 3-(N,N-DIMETHYLAMINO)ETHANOATE anchoring group
Analyse Pikc D50N mutant bound to the 10-dml analog with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZK5
- 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, Z18
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 hydroxylase pikc | protein | 397 | 53% helix, 10% strand | O87605 |
| B | Cytochrome P450 hydroxylase pikc | protein | 394 | 54% helix, 10% strand | O87605 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- Z18 · (3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl N,N-dimethylglycinate · 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 | 808 | 0.87 | 0.90 | 78 | HEM, Z18 |
| 2 | 808 | 0.87 | 0.89 | 75 | HEM, Z18 |
| 3 | 739 | 0.80 | 0.84 | 76 | empty |
| 4 | 51 | 0.30 | 0.76 | 10 | empty |
| 5 | 56 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ZK5 · PikC D50N mutant bound to the 10-DML analog with the 3-(N,N-dimethylamino)ethanoate… · 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 3ZK5 · PDBe 3ZK5 · UniProt O87605
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