Research workbench
Cholest-4-en-3-one bound structure of CYP142 from mycobacterium smegmatis
Analyse Cholest-4-en-3-one bound structure of CYP142 from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YOO
- Type
- protein
- Length
- 1,580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P450 heme-thiolate protein
- UniProt
- A0R4Q6
- Ligands
- HEM, K2B, MG
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P450 heme-thiolate protein | protein | 396 | 53% helix, 10% strand | A0R4Q6 |
| B, C | P450 heme-thiolate protein | protein | 395 | 53% helix, 10% strand | A0R4Q6 |
| D | P450 heme-thiolate protein | protein | 394 | 52% helix, 10% strand | A0R4Q6 |
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
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.86 | 0.87 | 113 | empty |
| 2 | 1116 | 0.86 | 0.87 | 109 | empty |
| 3 | 557 | 0.85 | 0.91 | 60 | HEM, K2B |
| 4 | 567 | 0.85 | 0.90 | 63 | HEM, K2B |
| 5 | 565 | 0.85 | 0.90 | 62 | HEM, K2B |
Interfaces
3 interfaces between chains.
- C–D · 1099 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1029 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YOO · Cholest-4-en-3-one bound structure of CYP142 from Mycobacterium smegmatis · the same entry in another collection · chain D against D, TM-score 1.00
- A0R4Q6 · AlphaFold monomer V2.0 prediction for steroid C26-monooxygenase (A0R4Q6) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A0R4Q6
- Elsewhere: RCSB PDB 2YOO · PDBe 2YOO · UniProt A0R4Q6
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