MolNFT v1 · #72483 · protein
Crystal structure of human CYP11A1 in complex with cholesterol
3N9Y · Cholesterol side-chain cleavage enzyme: “Crystal structure of human CYP11A1 in complex with cholesterol”. X-ray diffraction, 3 ligands (HEM, CLR, FES), 11 pockets (best druggability 0.88). MolNFT v1 #72483 on GenesisL1: 3D…
- PDB
- 3N9Y
- Type
- protein
- Length
- 1,077 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, CLR, FES
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholesterol side-chain cleavage enzyme (EC 1.14.15.6) | protein | 471 | 57% helix, 10% strand | P05108 |
| B | Cholesterol side-chain cleavage enzyme (EC 1.14.15.6) | protein | 470 | 58% helix, 10% strand | P05108 |
| C, D | Adrenodoxin | protein | 68 | 34% helix, 9% strand | P10109 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CLR · Cholesterol · 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.88 | 0.91 | 65 | HEM, CLR |
| 2 | 739 | 0.88 | 0.91 | 75 | HEM, CLR |
| 3 | 672 | 0.69 | 0.77 | 70 | empty |
| 4 | 275 | 0.66 | 0.83 | 43 | empty |
| 5 | 50 | 0.66 | 0.96 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1076 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1042 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3N9Y · Crystal structure of human CYP11A1 in complex with cholesterol · 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 0.96
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 P05108
- Every structure of UniProt P10109
- Elsewhere: RCSB PDB 3N9Y · PDBe 3N9Y · UniProt P05108 · UniProt P10109
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