Research workbench
Crystal structure of human CYP11A1 in complex with 20- hydroxycholesterol
Analyse Crystal structure of human CYP11A1 in complex with 20- hydroxycholesterol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NA1
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholesterol side-chain cleavage enzyme, mitochondrial; Adrenodoxin, mitochondrial
- EC
- 1.14.15.6
- UniProt
- P05108, P10109
- Ligands
- HEM, HCD, FES
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholesterol side-chain cleavage enzyme, mitochondrial (EC 1.14.15.6) | protein | 472 | 57% helix, 10% strand | P05108 |
| B | Cholesterol side-chain cleavage enzyme, mitochondrial (EC 1.14.15.6) | protein | 471 | 57% helix, 10% strand | P05108 |
| C | Adrenodoxin, mitochondrial | protein | 26 | 27% helix, 0% strand | P10109 |
| D | Adrenodoxin, mitochondrial | protein | 24 | 21% helix, 0% strand | P10109 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- HCD · (3alpha,8alpha)-cholest-5-ene-3,20-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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.88 | 0.91 | 81 | HEM, HCD |
| 2 | 774 | 0.87 | 0.90 | 83 | HEM, HCD |
| 3 | 699 | 0.69 | 0.77 | 75 | empty |
| 4 | 222 | 0.58 | 0.80 | 33 | empty |
| 5 | 149 | 0.57 | 0.82 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 884 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 870 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 352 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NA1 · Crystal structure of human CYP11A1 in complex with 20-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 A 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 0.75
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 3NA1 · PDBe 3NA1 · UniProt P05108 · UniProt P10109
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