Research workbench
Glycan binding protein Y3 from mushroom coprinus comatus possesses anti-leukemic activity - pt derivative
Analyse Glycan binding protein Y3 from mushroom coprinus comatus possesses… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6I
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tmv resistance protein Y3
- UniProt
- G3BK00
- Ligands
- PT, CL
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tmv resistance protein Y3 | protein | 112 | 25% helix, 31% strand | G3BK00 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 4 copies · chains B
- CL · Chloride ion · ion · 12 copies · chains B, A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.57 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1133 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5V6I · Glycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity… · 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 G3BK00
- Elsewhere: RCSB PDB 5V6I · PDBe 5V6I · UniProt G3BK00
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.