MolNFT v1 · #171707 · protein
Rifin variable region bound to LILRB1 ectodomain
6ZDX: “Rifin variable region bound to LILRB1 ectodomain”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.63). MolNFT v1 #171707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZDX
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rifin; Leukocyte immunoglobulin-like receptor subfamily B member 1
- UniProt
- Q8I4N9, A0A0G2JQ46
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rifin | protein | 100 | 71% helix, 1% strand | Q8I4N9 |
| B | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 396 | 4% helix, 45% strand | A0A0G2JQ46 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.63 | 0.80 | 30 | empty |
| 2 | 276 | 0.54 | 0.76 | 38 | empty |
| 3 | 69 | 0.35 | 0.76 | 12 | empty |
| 4 | 94 | 0.34 | 0.74 | 18 | empty |
| 5 | 53 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 777 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZDX · RIFIN variable region bound to LILRB1 ectodomain · 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 Q8I4N9
- Every structure of UniProt A0A0G2JQ46
- Elsewhere: RCSB PDB 6ZDX · PDBe 6ZDX · UniProt Q8I4N9 · UniProt A0A0G2JQ46
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