Research workbench
Human steroidogenic cytochrome P450 17A1 mutant A105L with substrate 17ALPHA-hydroxyprogesterone
Analyse Human steroidogenic cytochrome P450 17A1 mutant A105L with substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKY
- Type
- protein
- Length
- 1,858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid 17-alpha-HYDROXYLASE/17,20 lyase
- EC
- 1.14.99.9, 4.1.2.30
- UniProt
- P05093
- Ligands
- HEM, 3QZ
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Steroid 17-alpha-HYDROXYLASE/17,20 lyase (EC 1.14.99.9, 4.1.2.30) | protein | 462 | 51% helix, 10% strand | P05093 |
| B | Steroid 17-alpha-HYDROXYLASE/17,20 lyase (EC 1.14.99.9, 4.1.2.30) | protein | 464 | 50% helix, 11% strand | P05093 |
| C | Steroid 17-alpha-HYDROXYLASE/17,20 lyase (EC 1.14.99.9, 4.1.2.30) | protein | 467 | 49% helix, 11% strand | P05093 |
| D | Steroid 17-alpha-HYDROXYLASE/17,20 lyase (EC 1.14.99.9, 4.1.2.30) | protein | 465 | 49% helix, 11% strand | P05093 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 3QZ · (9beta)-17-hydroxypregn-4-ene-3,20-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.87 | 0.92 | 56 | HEM, 3QZ |
| 2 | 561 | 0.86 | 0.92 | 58 | HEM, 3QZ |
| 3 | 547 | 0.86 | 0.92 | 53 | HEM, 3QZ |
| 4 | 536 | 0.86 | 0.91 | 53 | HEM, 3QZ |
| 5 | 982 | 0.82 | 0.83 | 99 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2184 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2160 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 875 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 275 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 269 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NKY · Human steroidogenic cytochrome P450 17A1 mutant A105L with substrate… · the same entry in another collection · chain D against D, TM-score 1.00
- P05093 · AlphaFold monomer V2.0 prediction for steroid 17-alpha- HYDROXYLASE/17,20 lyase (P05093) · a predicted model of the same protein · chain D 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 P05093
- Elsewhere: RCSB PDB 4NKY · PDBe 4NKY · UniProt P05093
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