Research workbench
Pikc D50N mutant bound to the 10-dml analog with the 3-(N,N- DIMETHYLAMINO)PROPANOATE anchoring group
Analyse Pikc D50N mutant bound to the 10-dml analog with the 3-(N,N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B7S
- Type
- protein
- Length
- 790 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, SO4
- Pockets
- 4 · best druggability 0.88
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 | 397 | 54% helix, 10% strand | O87605 |
| B | Cytochrome P450 hydroxylase pikc | protein | 393 | 53% 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
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 7 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 | 856 | 0.88 | 0.90 | 76 | HEM, QLE, GOL |
| 2 | 927 | 0.86 | 0.88 | 83 | HEM, QLE, GOL |
| 3 | 948 | 0.80 | 0.82 | 83 | SO4 |
| 4 | 61 | 0.39 | 0.80 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4B7S · PikC D50N mutant bound to the 10-DML analog with the 3-(N,N- dimethylamino)propanoate… · 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 4B7S · PDBe 4B7S · UniProt O87605
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