MolNFT v1 · #32311 · protein
Modeling protein-substrate interactions in the heme domain of cytochrome P450BM-3
2BMH · Cytochrome P450 bm-3: “Modeling protein-substrate interactions in the heme domain of cytochrome P450BM-3”. X-ray diffraction, 1 ligand (HEM), 8 pockets (best druggability 0.85). MolNFT v1 #32311 on GenesisL1: 3D structure, binding…
- PDB
- 2BMH
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 bm-3
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 bm-3 (EC 1.14.14.1) | protein | 455 | 55% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.85 | 0.85 | 104 | HEM |
| 2 | 1145 | 0.85 | 0.85 | 121 | HEM |
| 3 | 427 | 0.57 | 0.74 | 56 | empty |
| 4 | 232 | 0.51 | 0.75 | 28 | empty |
| 5 | 245 | 0.51 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2BMH · Modeling protein-substrate interactions in the heme domain of cytochrome P450BM-3 · 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 2BMH · PDBe 2BMH · UniProt P14779
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