Research workbench
Crystal structure of CYP124 in complex with cholest-4-en-3-one
Analyse Crystal structure of CYP124 in complex with cholest-4-en-3-one in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T0F
- Type
- protein
- Length
- 1,722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- Methyl-branched lipid omega-hydroxylase
- EC
- 1.14.15.14, 1.14.15.28
- UniProt
- P9WPP3
- Ligands
- HEM, K2B
- Pockets
- 14 · best druggability 0.90
Structure
x-ray diffraction · resolution 1.65 · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-branched lipid omega-hydroxylase (EC 1.14.15.14, 1.14.15.28) | protein | 431 | 50% helix, 11% strand | P9WPP3 |
| B, C | Methyl-branched lipid omega-hydroxylase (EC 1.14.15.14, 1.14.15.28) | protein | 430 | 50% helix, 11% strand | P9WPP3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- K2B · (8alpha,9beta)-cholest-4-en-3-one · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.90 | 0.94 | 77 | HEM, K2B |
| 2 | 672 | 0.90 | 0.94 | 81 | HEM, K2B |
| 3 | 676 | 0.90 | 0.94 | 75 | HEM, K2B |
| 4 | 680 | 0.89 | 0.94 | 83 | HEM, K2B |
| 5 | 1019 | 0.81 | 0.82 | 120 | MPO |
Interfaces
5 interfaces between chains.
- C–D · 667 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6T0F · Crystal structure of CYP124 in complex with cholest-4-en-3-one · the same entry in another collection · chain D against D, TM-score 1.00
- P9WPP3 · AlphaFold monomer V2.0 prediction for methyl-branched lipid omega- hydroxylase (P9WPP3) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P9WPP3
- Elsewhere: RCSB PDB 6T0F · PDBe 6T0F · UniProt P9WPP3
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