Research workbench
Crystal structure of the variable region of plasmodium rifin #4 (PF3D7_1000500) in complex with LAIR1
Analyse Crystal structure of the variable region of plasmodium rifin #4 (PF3D7_1000500)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F9N
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rifin; Leukocyte-associated immunoglobulin-like receptor 1
- UniProt
- A0A143ZWD5, Q6GTX8
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rifin | protein | 158 | 76% helix, 0% strand | A0A143ZWD5 |
| C | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 98 | 3% helix, 49% strand | Q6GTX8 |
| D | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 97 | 3% helix, 55% strand | Q6GTX8 |
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 | 52 | 0.57 | 0.90 | 18 | empty |
| 2 | 59 | 0.39 | 0.80 | 14 | empty |
| 3 | 91 | 0.36 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 884 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 861 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7F9N · Crystal structure of the variable region of Plasmodium RIFIN #4 (PF3D7_1000500) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GTX8 · AlphaFold monomer V2.0 prediction for leukocyte-associated immunoglobulin-like receptor 1… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 A0A143ZWD5
- Every structure of UniProt Q6GTX8
- Elsewhere: RCSB PDB 7F9N · PDBe 7F9N · UniProt A0A143ZWD5 · UniProt Q6GTX8
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