Research workbench
Haddock model of the complex between double module of lrp, CR56, and first domain of receptor associated protein, rap-D1.
Analyse Haddock model of the complex between double module of lrp, CR56, and first… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FYL
- Type
- protein
- Length
- 163 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin receptor-associated protein; Low-density lipoprotein…
- UniProt
- P30533, Q07954
- Ligands
- CA
- Pockets
- 1 · best druggability 0.74
Structure
solution nmr · 2 distinct chains · 36% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-2-macroglobulin receptor-associated protein | protein | 81 | 69% helix, 0% strand | P30533 |
| B | Low-density lipoprotein receptor-related protein 1 | protein | 82 | 4% helix, 15% strand | Q07954 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.74 | 0.81 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2FYL · Haddock model of the complex between double module of LRP, CR56, and first domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- P30533 · AlphaFold monomer V2.0 prediction for alpha-2-macroglobulin receptor- associated protein… · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P30533
- Every structure of UniProt Q07954
- Elsewhere: RCSB PDB 2FYL · PDBe 2FYL · UniProt P30533 · UniProt Q07954
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