MolNFT v1 · #116112 · protein
Crystal structure of the 5-selective H176F mutant of cytochrome txte
5D3U · P450-like protein: “Crystal structure of the 5-selective H176F mutant of cytochrome txte”. X-ray diffraction, 3 ligands (HEM, TRP, CL), 6 pockets (best druggability 0.87). MolNFT v1 #116112 on GenesisL1: 3D structure, binding sites…
- PDB
- 5D3U
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P450-like protein
- UniProt
- C9ZDC6
- Ligands
- HEM, TRP, CL
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | P450-like protein | protein | 403 | 54% helix, 10% strand | C9ZDC6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.87 | 0.93 | 66 | HEM, TRP |
| 2 | 437 | 0.86 | 0.93 | 56 | HEM, TRP |
| 3 | 244 | 0.56 | 0.78 | 29 | empty |
| 4 | 242 | 0.56 | 0.78 | 27 | empty |
| 5 | 91 | 0.38 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D3U · Crystal structure of the 5-selective H176F mutant of Cytochrome TxtE · the same entry in another collection · chain A against A, TM-score 1.00
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 C9ZDC6
- Elsewhere: RCSB PDB 5D3U · PDBe 5D3U · UniProt C9ZDC6
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