MolNFT v1 · #135988 · protein
Crystal structure of variable lymphocyte receptor (vlr) TN4-22 with H- trisaccharide bound
5UFC: “Crystal structure of variable lymphocyte receptor (vlr) TN4-22 with H- trisaccharide bound”. X-ray diffraction, 3 ligands (NAG, GAL, FUC), 4 pockets (best druggability 0.48). MolNFT v1 #135988 on GenesisL1: 3D structure, binding…
- PDB
- 5UFC
- Type
- protein
- Length
- 720 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TN4-22
- Ligands
- NAG, GAL, FUC
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | TN4-22 | protein | 240 | 11% helix, 16% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.48 | 0.74 | 27 | empty |
| 2 | 176 | 0.45 | 0.75 | 25 | empty |
| 3 | 54 | 0.27 | 0.73 | 14 | GAL |
| 4 | 51 | 0.27 | 0.73 | 12 | GAL |
Interfaces
2 interfaces between chains.
- A–B · 646 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 625 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5UFC · Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 with H-trisaccharide bound · 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
- Elsewhere: RCSB PDB 5UFC · PDBe 5UFC
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