Research workbench
Crystal structure of cytochrome P450 CYP121, P212121 space group
Analyse Crystal structure of cytochrome P450 CYP121, P212121 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IJ5
- Type
- protein
- Length
- 2,338 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 121
- EC
- 1.14.-.-
- UniProt
- P0A514
- Ligands
- HEM, SO4
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 121 (EC 1.14.-.-) | protein | 392 | 52% helix, 11% strand | P0A514 |
| B | Cytochrome P450 121 (EC 1.14.-.-) | protein | 390 | 52% helix, 11% strand | P0A514 |
| C | Cytochrome P450 121 (EC 1.14.-.-) | protein | 394 | 52% helix, 10% strand | P0A514 |
| D | Cytochrome P450 121 (EC 1.14.-.-) | protein | 391 | 52% helix, 11% strand | P0A514 |
| E | Cytochrome P450 121 (EC 1.14.-.-) | protein | 387 | 50% helix, 11% strand | P0A514 |
| F | Cytochrome P450 121 (EC 1.14.-.-) | protein | 384 | 52% helix, 11% strand | P0A514 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.87 | 0.89 | 86 | SO4, HEM |
| 2 | 880 | 0.87 | 0.89 | 74 | HEM |
| 3 | 857 | 0.87 | 0.89 | 79 | HEM |
| 4 | 854 | 0.87 | 0.89 | 71 | HEM |
| 5 | 883 | 0.86 | 0.88 | 76 | HEM |
Interfaces
4 interfaces between chains.
- D–E · 427 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 345 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 307 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 167 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2IJ5 · Crystal structure of cytochrome P450 CYP121, P212121 space group · 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 P0A514
- Elsewhere: RCSB PDB 2IJ5 · PDBe 2IJ5 · UniProt P0A514
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