MolNFT v1 · #135978 · protein
Crystal structure of variable lymphocyte receptor (vlr) O13 in complex with H-trisaccharide
5UF1: “Crystal structure of variable lymphocyte receptor (vlr) O13 in complex with H-trisaccharide”. X-ray diffraction, 4 ligands (NAG, GAL, FUC), 3 pockets (best druggability 0.69). MolNFT v1 #135978 on GenesisL1: 3D structure, binding…
- PDB
- 5UF1
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O13
- Ligands
- NAG, GAL, FUC, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | O13 | protein | 241 | 11% helix, 17% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, A
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.69 | 0.78 | 60 | NAG, GAL, FUC |
| 2 | 96 | 0.38 | 0.75 | 16 | GAL |
| 3 | 57 | 0.34 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 585 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5UF1 · Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 in complex with… · the same entry in another collection · chain B against B, 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 5UF1 · PDBe 5UF1
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