MolNFT v1 · #123648 · protein
Crystal structure of cytochrome P450 BM3 heme domain T269V/L272W/L322I/A406S (wivs) variant with IRON(III) deuteroporphyrin IX bound
5JQV · Bifunctional cytochrome P450/NADPH--P450 reductase: “Crystal structure of cytochrome P450 BM3 heme domain T269V/L272W/L322I/A406S (wivs) variant with IRON(III)…”. X-ray diffraction, 1 ligand (FDE), 20 pockets (best druggability…
- PDB
- 5JQV
- Type
- protein
- Length
- 3,619 residues
- Chains
- 8
- 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
- FDE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 453 | 54% helix, 11% strand | P14779 |
| B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 453 | 53% helix, 11% strand | P14779 |
| C | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 452 | 53% helix, 11% strand | P14779 |
| D | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 454 | 54% helix, 11% strand | P14779 |
| E | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 451 | 54% helix, 12% strand | P14779 |
| F | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 455 | 53% helix, 12% strand | P14779 |
| G | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 451 | 54% helix, 11% strand | P14779 |
| H | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 450 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- FDE · Fe(iii) deuteroporphyrin IX · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.88 | 0.93 | 85 | FDE |
| 2 | 699 | 0.88 | 0.92 | 84 | FDE |
| 3 | 624 | 0.88 | 0.93 | 83 | FDE |
| 4 | 727 | 0.88 | 0.91 | 85 | FDE |
| 5 | 651 | 0.88 | 0.92 | 85 | FDE |
Interfaces
15 interfaces between chains.
- B–C · 983 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 886 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 575 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 511 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 421 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5JQV · Crystal structure of Cytochrome P450 BM3 heme domain T269V/L272W/L322I/A406S (WIVS)… · the same entry in another collection · chain H against H, 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 A against A, TM-score 0.98
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 5JQV · PDBe 5JQV · UniProt P14779
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