MolNFT v1 · #150380 · protein
Paired immunoglobulin-like receptor B (pirb) or leukocyte immunoglobulin-like receptor subfamily B member 3 (LILRB3) full extracellular domain
6GRT: “Paired immunoglobulin-like receptor B (pirb) or leukocyte immunoglobulin-like receptor subfamily B member 3…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 11 pockets (best druggability 0.50). MolNFT v1 #150380 on GenesisL1: 3D…
- PDB
- 6GRT
- Type
- protein
- Length
- 1,187 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paired immunoglobulin-like receptor B
- UniProt
- Q8K4V6
- Ligands
- NAG, BMA, MAN
- Pockets
- 11 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paired immunoglobulin-like receptor B | protein | 593 | 2% helix, 48% strand | Q8K4V6 |
| B | Paired immunoglobulin-like receptor B | protein | 594 | 2% helix, 46% strand | Q8K4V6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.50 | 0.79 | 22 | empty |
| 2 | 176 | 0.45 | 0.75 | 25 | empty |
| 3 | 116 | 0.43 | 0.77 | 16 | empty |
| 4 | 127 | 0.42 | 0.76 | 25 | empty |
| 5 | 122 | 0.41 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6GRT · Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunoglobulin-like receptor… · 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
- Every structure of UniProt Q8K4V6
- Elsewhere: RCSB PDB 6GRT · PDBe 6GRT · UniProt Q8K4V6
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