MolNFT v1 · #179240 · protein
Crystal structure of LAIR1 ectodomain (from MGD21) in complex with plasmodium rifin (PF3D7_0401300) V2 domain
7JZK · LAIR1 ecotodomain from MGD21 antibody: “Crystal structure of LAIR1 ectodomain (from MGD21) in complex with plasmodium rifin (PF3D7_0401300) V2 domain”. X-ray diffraction, 2 ligands (NAG, BMA), 3 pockets (best druggability 0.69).…
- PDB
- 7JZK
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LAIR1 ecotodomain from MGD21 antibody; Rifin
- UniProt
- W7K133
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | LAIR1 ecotodomain from MGD21 antibody | protein | 98 | 3% helix, 52% strand | — |
| D | Rifin | protein | 116 | 66% helix, 4% strand | W7K133 |
| A | LAIR1 ecotodomain from MGD21 antibody | protein | 105 | 3% helix, 52% strand | — |
| B | Rifin | protein | 123 | 68% helix, 3% strand | W7K133 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
- BMA · beta-D-mannopyranose · sugar
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 | 494 | 0.69 | 0.79 | 67 | empty |
| 2 | 66 | 0.31 | 0.75 | 15 | empty |
| 3 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1034 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 15 hydrogen bonds · protein-protein
- D–B · 387 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 343 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JZK · Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN… · the same entry in another collection · chain C against C, 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 W7K133
- Elsewhere: RCSB PDB 7JZK · PDBe 7JZK · UniProt W7K133
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