MolNFT v1 · #117338 · protein
Crystal structure of cytochrome P450 2B35 from desert woodrat neotoma lepida in complex with 4-(4-CHLOROPHENYL)IMIDAZOLE
5E58 · Cytochrome P450 family 2 subfamily B: “Crystal structure of cytochrome P450 2B35 from desert woodrat neotoma lepida in complex with…”. X-ray diffraction, 5 ligands (CPZ, HEM, CM5), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 5E58
- Type
- protein
- Length
- 2,770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 family 2 subfamily B
- UniProt
- J9JD66
- Ligands
- CPZ, HEM, CM5, GLC, FRU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 family 2 subfamily B | protein | 464 | 51% helix, 10% strand | J9JD66 |
| B | Cytochrome P450 family 2 subfamily B | protein | 458 | 51% helix, 10% strand | J9JD66 |
| C | Cytochrome P450 family 2 subfamily B | protein | 465 | 51% helix, 9% strand | J9JD66 |
| D | Cytochrome P450 family 2 subfamily B | protein | 463 | 52% helix, 10% strand | J9JD66 |
| E | Cytochrome P450 family 2 subfamily B | protein | 462 | 51% helix, 10% strand | J9JD66 |
| F | Cytochrome P450 family 2 subfamily B | protein | 458 | 51% helix, 11% strand | J9JD66 |
Ligands and binding sites
- CPZ · 4-(4-chlorophenyl)imidazole · ligand · 12 copies · chains A, B, C, D, E, F
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 2 copies · chains A, E
- GLC · alpha-D-glucopyranose · sugar · chains A, D
- FRU · beta-D-fructofuranose · sugar · chains A, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, E
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 | 607 | 0.87 | 0.92 | 59 | HEM, CPZ |
| 2 | 587 | 0.87 | 0.92 | 54 | HEM, CPZ |
| 3 | 558 | 0.87 | 0.92 | 53 | HEM, CPZ |
| 4 | 570 | 0.86 | 0.92 | 55 | HEM, CPZ |
| 5 | 571 | 0.86 | 0.92 | 56 | HEM, CPZ |
Interfaces
8 interfaces between chains.
- A–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 558 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 494 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 290 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 267 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5E58 · Crystal Structure Of Cytochrome P450 2B35 from Desert Woodrat Neotoma Lepida in 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 J9JD66
- Elsewhere: RCSB PDB 5E58 · PDBe 5E58 · UniProt J9JD66
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