MolNFT v1 · #139253 · protein
Crystal structure of P450BM3 with benzyloxycarbonyl-L-prolyl-L- phenylalanine
5XA3 · Bifunctional cytochrome P450/NADPH-P450 reductase: “Crystal structure of P450BM3 with benzyloxycarbonyl-L-prolyl-L- phenylalanine”. X-ray diffraction, 2 ligands (HEM, PHQ), 20 pockets (best druggability 0.87). MolNFT v1 #139253 on…
- PDB
- 5XA3
- Type
- protein
- Length
- 1,820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cytochrome P450/NADPH-P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, PHQ
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bifunctional cytochrome P450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 455 | 53% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PHQ · benzyl chlorocarbonate · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.87 | 0.94 | 65 | HEM, DMS, PHQ |
| 2 | 474 | 0.87 | 0.93 | 66 | HEM, DMS, PHQ |
| 3 | 484 | 0.86 | 0.92 | 70 | HEM, DMS, PHQ |
| 4 | 526 | 0.86 | 0.92 | 74 | HEM, DMS, PHQ |
| 5 | 1104 | 0.81 | 0.82 | 80 | empty |
Interfaces
3 interfaces between chains.
- B–D · 884 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 753 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5XA3 · Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine · the same entry in another collection · chain D against D, TM-score 1.00
- P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P14779
- Elsewhere: RCSB PDB 5XA3 · PDBe 5XA3 · UniProt P14779
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