MolNFT v1 · #55521 · protein
Crystal structure of chicken galectin 2
2YMZ: “Crystal structure of chicken galectin 2”. X-ray diffraction, 3 ligands (BGC, GAL, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #55521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YMZ
- Type
- protein
- Length
- 780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin 2
- UniProt
- E1C0Z4
- Ligands
- BGC, GAL, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Galectin 2 | protein | 130 | 0% helix, 62% strand | E1C0Z4 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, F
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 | 383 | 0.78 | 0.87 | 56 | empty |
| 2 | 376 | 0.76 | 0.86 | 50 | empty |
| 3 | 357 | 0.71 | 0.83 | 45 | empty |
| 4 | 390 | 0.69 | 0.82 | 39 | empty |
| 5 | 62 | 0.50 | 0.86 | 17 | empty |
Interfaces
10 interfaces between chains.
- D–E · 705 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 700 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 700 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 420 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2YMZ · Crystal structure of chicken Galectin 2 · 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 E1C0Z4
- Elsewhere: RCSB PDB 2YMZ · PDBe 2YMZ · UniProt E1C0Z4
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