Research workbench
Crystal structure of human cytochrome P450 21A2 hydroxyprogesterone complex
Analyse Crystal structure of human cytochrome P450 21A2 hydroxyprogesterone complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VBU
- Type
- protein
- Length
- 1,325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 21-hydroxylase
- UniProt
- Q16874
- Ligands
- HEM, 3QZ
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome P450 21-hydroxylase | protein | 442 | 53% helix, 10% strand | Q16874 |
| B | Cytochrome P450 21-hydroxylase | protein | 441 | 53% helix, 10% strand | Q16874 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- 3QZ · (9beta)-17-hydroxypregn-4-ene-3,20-dione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.88 | 0.90 | 96 | HEM, 3QZ |
| 2 | 500 | 0.86 | 0.92 | 59 | HEM, 3QZ |
| 3 | 1137 | 0.86 | 0.87 | 101 | HEM, 3QZ |
| 4 | 1198 | 0.83 | 0.84 | 86 | empty |
| 5 | 1111 | 0.82 | 0.83 | 79 | empty |
Interfaces
3 interfaces between chains.
- A–C · 707 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 573 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VBU · Crystal Structure of Human Cytochrome P450 21A2 Hydroxyprogesterone Complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q16874
- Elsewhere: RCSB PDB 5VBU · PDBe 5VBU · UniProt Q16874
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