MolNFT v1 · #72484 · protein
Crystal structure of human CYP11A1 in complex with 22- hydroxycholesterol
3N9Z · Cholesterol side-chain cleavage enzyme: “Crystal structure of human CYP11A1 in complex with 22- hydroxycholesterol”. X-ray diffraction, 3 ligands (HEM, HC9, FES), 13 pockets (best druggability 0.88). MolNFT v1 #72484 on GenesisL1…
- PDB
- 3N9Z
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholesterol side-chain cleavage enzyme; Adrenodoxin
- EC
- 1.14.15.6
- UniProt
- P05108, P10109
- Ligands
- HEM, HC9, FES
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cholesterol side-chain cleavage enzyme (EC 1.14.15.6) | protein | 470 | 58% helix, 10% strand | P05108 |
| C, D | Adrenodoxin | protein | 27 | 22% helix, 7% strand | P10109 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- HC9 · (3alpha,8alpha,22R)-cholest-5-ene-3,22-diol · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.88 | 0.91 | 72 | HEM, HC9 |
| 2 | 804 | 0.87 | 0.90 | 73 | HEM, HC9 |
| 3 | 401 | 0.65 | 0.79 | 47 | empty |
| 4 | 242 | 0.65 | 0.82 | 39 | empty |
| 5 | 217 | 0.62 | 0.82 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 924 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3N9Z · Crystal structure of human CYP11A1 in complex with 22-hydroxycholesterol · the same entry in another collection · chain D against D, TM-score 1.00
- P05108 · AlphaFold monomer V2.0 prediction for cholesterol side-chain cleavage enzyme… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P10109 · AlphaFold monomer V2.0 prediction for adrenodoxin, mitochondrial (P10109) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 P05108
- Every structure of UniProt P10109
- Elsewhere: RCSB PDB 3N9Z · PDBe 3N9Z · UniProt P05108 · UniProt P10109
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