MolNFT v1 · #15116 · protein
X-ray crystal structure of rattlesnake venom complexed with thiodigalactoside
1MUQ · Galactose-specific lectin: “X-ray crystal structure of rattlesnake venom complexed with thiodigalactoside”. X-ray diffraction, 4 ligands (YIO, GAL, CA), 7 pockets (best druggability 0.38). MolNFT v1 #15116 on GenesisL1: 3D…
- PDB
- 1MUQ
- Type
- protein
- Length
- 670 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-specific lectin
- UniProt
- P21963
- Ligands
- YIO, GAL, CA, NA
- Pockets
- 7 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Galactose-specific lectin | protein | 134 | 23% helix, 32% strand | P21963 |
Ligands and binding sites
- YIO · 1-thio-beta-D-galactopyranose · ligand · chains B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, C, E
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.38 | 0.75 | 21 | empty |
| 2 | 108 | 0.36 | 0.74 | 19 | empty |
| 3 | 95 | 0.36 | 0.75 | 18 | empty |
| 4 | 89 | 0.32 | 0.74 | 20 | empty |
| 5 | 85 | 0.31 | 0.73 | 24 | empty |
Interfaces
5 interfaces between chains.
- D–E · 637 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 627 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 626 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 625 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 1MUQ · X-ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside · the same entry in another collection · chain A against A, TM-score 1.00
- P21963 · AlphaFold monomer V2.0 prediction for C-type lectin cal (P21963) · 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 P21963
- Elsewhere: RCSB PDB 1MUQ · PDBe 1MUQ · UniProt P21963
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