Research workbench
Crystal structure of P450 BM3 heme domain variant complexed with CO(III)SEP
Analyse Crystal structure of P450 BM3 heme domain variant complexed with CO(III)SEP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E78
- Type
- protein
- Length
- 901 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, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, 5KK, CO, CL
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 447 | 55% helix, 11% strand | P14779 |
| B | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 454 | 55% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 5KK · 1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]icosane · ligand · chains B
- CO · Cobalt (II) ion · metal · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.88 | 0.91 | 80 | HEM |
| 2 | 987 | 0.86 | 0.86 | 90 | HEM |
| 3 | 267 | 0.76 | 0.89 | 38 | empty |
| 4 | 223 | 0.56 | 0.78 | 27 | empty |
| 5 | 218 | 0.55 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5E78 · Crystal structure of P450 BM3 heme domain variant complexed with Co(III)Sep · 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 0.99
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 5E78 · PDBe 5E78 · UniProt P14779
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