MolNFT v1 · #56085 · protein
The Y66L mutant of tetraheme cytochrome C3 from desulfovibrio vulgaris miyazaki F
2Z47: “The Y66L mutant of tetraheme cytochrome C3 from desulfovibrio vulgaris miyazaki F”. X-ray diffraction, 1 ligand (HEC), 2 pockets (best druggability 0.76). MolNFT v1 #56085 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2Z47
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C3
- UniProt
- P00132
- Ligands
- HEC
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C3 | protein | 107 | 29% helix, 11% strand | P00132 |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.76 | 0.80 | 81 | HEC |
| 2 | 694 | 0.75 | 0.81 | 69 | HEC |
Interfaces
1 interface between chains.
- A–B · 236 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme c attachment).
Compared structures
- 2Z47 · The Y66L mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F · the same entry in another collection · chain A against A, TM-score 1.00
- P00132 · AlphaFold monomer V2.0 prediction for cytochrome C3 (P00132) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00132
- Elsewhere: RCSB PDB 2Z47 · PDBe 2Z47 · UniProt P00132
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