Research workbench
Crystal structure of rat galectin 5
Analyse Crystal structure of rat galectin 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JP5
- Type
- protein
- Length
- 834 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-5
- UniProt
- P47967
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Galectin-5 | protein | 134 | 2% helix, 55% strand | P47967 |
| D, E, F | Galectin-5 | protein | 144 | 2% helix, 53% strand | P47967 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.74 | 0.84 | 62 | empty |
| 2 | 460 | 0.67 | 0.79 | 44 | empty |
| 3 | 578 | 0.63 | 0.75 | 50 | empty |
| 4 | 203 | 0.45 | 0.74 | 27 | PEG |
| 5 | 72 | 0.30 | 0.73 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–E · 460 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 455 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 410 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 395 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 379 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- P47967 · AlphaFold monomer V2.0 prediction for galectin-5 (P47967) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P47967
- Elsewhere: RCSB PDB 5JP5 · PDBe 5JP5 · UniProt P47967
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