Research workbench
Crystal structure of LILRB1 D3D4 domain in complex with plasmodium rifin (PF3D7_1373400) V2 domain
Analyse Crystal structure of LILRB1 D3D4 domain in complex with plasmodium rifin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KFK
- Type
- protein
- Length
- 671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of leukocyte immunoglobulin-like receptor subfamily B member 1; Rifin
- UniProt
- C0H5N9
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoform 2 of leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 207 | 3% helix, 50% strand | — |
| E | Rifin | protein | 125 | 66% helix, 4% strand | C0H5N9 |
| C | Rifin | protein | 132 | 64% helix, 4% strand | C0H5N9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.68 | 0.89 | 29 | empty |
| 2 | 394 | 0.59 | 0.76 | 54 | SO4 |
| 3 | 97 | 0.59 | 0.87 | 32 | empty |
| 4 | 175 | 0.49 | 0.77 | 26 | empty |
| 5 | 113 | 0.38 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1059 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 971 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 223 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7KFK · Crystal structure of LILRB1 D3D4 domain in complex with Plasmodium RIFIN (PF3D7_1373400)… · 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 C0H5N9
- Elsewhere: RCSB PDB 7KFK · PDBe 7KFK · UniProt C0H5N9
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