MolNFT v1 · #72556 · protein
CYP134A1 structure with an open substrate binding loop
3NC5 · Cytochrome P450 cypx: “CYP134A1 structure with an open substrate binding loop”. X-ray diffraction, 2 ligands (HEM, MG), 7 pockets (best druggability 0.85). MolNFT v1 #72556 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3NC5
- Type
- protein
- Length
- 757 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 cypx
- EC
- 1.14.-.-
- UniProt
- O34926
- Ligands
- HEM, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 cypx (EC 1.14.-.-) | protein | 384 | 52% helix, 10% strand | O34926 |
| B | Cytochrome P450 cypx (EC 1.14.-.-) | protein | 373 | 54% helix, 9% strand | O34926 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.85 | 0.88 | 59 | HEM, GOL |
| 2 | 874 | 0.82 | 0.84 | 70 | HEM, GOL |
| 3 | 162 | 0.48 | 0.77 | 27 | empty |
| 4 | 175 | 0.46 | 0.75 | 28 | empty |
| 5 | 195 | 0.46 | 0.74 | 35 | MG |
Interfaces
1 interface between chains.
- A–B · 735 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 O34926
- Elsewhere: RCSB PDB 3NC5 · PDBe 3NC5 · UniProt O34926
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