MolNFT v1 · #62602 · protein
Crystal structure of the A264M heme domain of cytochrome P450 BM3
3EKD · Cytochrome P450(BM-3): “Crystal structure of the A264M heme domain of cytochrome P450 BM3”. X-ray diffraction, 2 ligands (HEM, PAM), 9 pockets (best druggability 0.89). MolNFT v1 #62602 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EKD
- Type
- protein
- Length
- 909 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, PAM
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450(BM-3) (EC 1.14.14.1) | protein | 454 | 53% helix, 11% strand | P14779 |
| B | Cytochrome P450(BM-3) (EC 1.14.14.1) | protein | 455 | 52% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PAM · Palmitoleic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.89 | 0.90 | 93 | PAM, HEM |
| 2 | 1092 | 0.88 | 0.89 | 98 | HEM |
| 3 | 189 | 0.58 | 0.81 | 29 | empty |
| 4 | 209 | 0.57 | 0.80 | 27 | empty |
| 5 | 221 | 0.48 | 0.74 | 32 | empty |
Compared structures
- 3EKD · Crystal structure of the A264M heme domain of cytochrome P450 BM3 · 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 0.97
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 3EKD · PDBe 3EKD · UniProt P14779
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