Research workbench
Cytochrome P450 BM3H-2G9 mri sensor bound to serotonin
Analyse Cytochrome P450 BM3H-2G9 mri sensor bound to serotonin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DUF
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 BM3 variant 2G9
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM, SRO
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome P450 BM3 variant 2G9 (EC 1.14.14.1) | protein | 456 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SRO · Serotonin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.89 | 0.90 | 113 | HEM, SRO |
| 2 | 1186 | 0.88 | 0.89 | 131 | HEM, SRO |
| 3 | 896 | 0.85 | 0.87 | 87 | HEM, SRO |
| 4 | 1085 | 0.85 | 0.86 | 107 | HEM, SRO |
| 5 | 472 | 0.72 | 0.81 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–C · 713 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 706 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 462 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 194 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 138 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4DUF · cytochrome P450 BM3h-2G9 MRI sensor bound to serotonin · 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 4DUF · PDBe 4DUF · UniProt P14779
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