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Crystal structure of LAIR1 ectodomain (from MGD21) in complex with plasmodium rifin (PF3D7_1040300) V2 domain
Analyse Crystal structure of LAIR1 ectodomain (from MGD21) in complex with plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZI
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LAIR1 ectodomain from antibody MGD21; Rifin
- UniProt
- A0A2I0BRG0
- Ligands
- PT
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | LAIR1 ectodomain from antibody MGD21 | protein | 98 | 0% helix, 49% strand | — |
| B | Rifin | protein | 122 | 75% helix, 0% strand | A0A2I0BRG0 |
| D | Rifin | protein | 132 | 75% helix, 0% strand | A0A2I0BRG0 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 2 copies · chains B, D
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 | 358 | 0.69 | 0.82 | 51 | empty |
| 2 | 71 | 0.35 | 0.77 | 15 | empty |
| 3 | 62 | 0.33 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 972 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 944 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 378 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JZI · Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN… · 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 A0A2I0BRG0
- Elsewhere: RCSB PDB 7JZI · PDBe 7JZI · UniProt A0A2I0BRG0
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