MolNFT v1 · #29944 · protein
Crystal structure of the wild type heme domain of P450BM-3 with N- palmitoylmethionine
1ZO9 · Bifunctional P-450:NADPH-P450 reductase: “Crystal structure of the wild type heme domain of P450BM-3 with N- palmitoylmethionine”. X-ray diffraction, 2 ligands (HEM, EPM), 8 pockets (best druggability 0.90). MolNFT v1 #29944 on…
- PDB
- 1ZO9
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional P-450:NADPH-P450 reductase
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM, EPM
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional P-450:NADPH-P450 reductase (EC 1.14.14.1) | protein | 458 | 52% helix, 12% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- EPM · N-palmitoyl-L-methionine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 14 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.90 | 0.92 | 109 | HEM, EPM |
| 2 | 756 | 0.87 | 0.90 | 90 | HEM, EPM |
| 3 | 171 | 0.58 | 0.82 | 25 | empty |
| 4 | 150 | 0.55 | 0.81 | 26 | GOL |
| 5 | 57 | 0.54 | 0.89 | 9 | GOL |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1ZO9 · Crystal Structure Of The Wild Type Heme Domain Of P450BM-3 with N-palmitoylmethionine · the same entry in another collection · chain A against A, 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 1ZO9 · PDBe 1ZO9 · UniProt P14779
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