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Crystal structure of A328V mutant of the heme domain of P450BM-3 with N-palmitoylglycine
Analyse Crystal structure of A328V mutant of the heme domain of P450BM-3 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZOA
- Type
- protein
- Length
- 914 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, 140
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 53% 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 | 457 | 53% helix, 12% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 140 · N-palmitoylglycine · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.89 | 0.90 | 121 | HEM, 140 |
| 2 | 660 | 0.87 | 0.91 | 85 | HEM, 140 |
| 3 | 219 | 0.60 | 0.81 | 26 | empty |
| 4 | 179 | 0.58 | 0.81 | 25 | empty |
| 5 | 171 | 0.51 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1ZOA · Crystal Structure Of A328V Mutant Of The Heme Domain Of P450Bm-3 With N-Palmitoylglycine · 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 B 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 1ZOA · PDBe 1ZOA · UniProt P14779
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