MolNFT v1 · #135981 · protein
Crystal structure of variable lymphocyte receptor (vlr) O13 with lnnt bound
5UF4: “Crystal structure of variable lymphocyte receptor (vlr) O13 with lnnt bound”. X-ray diffraction, 3 ligands (GAL, GLC, NAG), 5 pockets (best druggability 0.57). MolNFT v1 #135981 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5UF4
- Type
- protein
- Length
- 723 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O13
- Ligands
- GAL, GLC, NAG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | O13 | protein | 241 | 10% helix, 17% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.57 | 0.78 | 33 | empty |
| 2 | 312 | 0.50 | 0.73 | 38 | empty |
| 3 | 96 | 0.37 | 0.75 | 17 | GAL |
| 4 | 81 | 0.37 | 0.76 | 17 | GAL |
| 5 | 71 | 0.33 | 0.75 | 16 | GAL |
Interfaces
2 interfaces between chains.
- A–B · 127 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5UF4 · Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 with LNnT 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 5UF4 · PDBe 5UF4
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