Research workbench
Crystal structure of cytochrome C - P-SULFONATOCALIX[4]ARENE complexes
Analyse Crystal structure of cytochrome C - P-SULFONATOCALIX[4]ARENE complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TYI
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- T3Y, HEM
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C iso-1 | protein | 108 | 41% helix, 2% strand | P00044 |
Ligands and binding sites
- T3Y · 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9, 13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12, 15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid · ligand · 3 copies · chains A, B
- 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.76 | 0.91 | 35 | HEM |
| 2 | 173 | 0.73 | 0.90 | 30 | HEM |
| 3 | 138 | 0.48 | 0.78 | 19 | empty |
| 4 | 127 | 0.43 | 0.77 | 19 | empty |
| 5 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 3TYI · Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes · the same entry in another collection · chain A against A, TM-score 1.00
- P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · 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 P00044
- Elsewhere: RCSB PDB 3TYI · PDBe 3TYI · UniProt P00044
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