Research workbench
Crystal structure of agrin and LRP4
Analyse Crystal structure of agrin and LRP4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V64
- Type
- protein
- Length
- 1,053 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 4; Agrin
- UniProt
- Q9QYP1, P25304
- Ligands
- NAG, CA, PO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Low-density lipoprotein receptor-related protein 4 | protein | 338 | 3% helix, 46% strand | Q9QYP1 |
| A | Agrin | protein | 191 | 4% helix, 46% strand | P25304 |
| B | Agrin | protein | 190 | 4% helix, 44% strand | P25304 |
| D | Low-density lipoprotein receptor-related protein 4 | protein | 334 | 1% helix, 47% strand | Q9QYP1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- CA · Calcium ion · metal · 5 copies · chains C, A, B, D
- PO4 · Phosphate ion · ion · 4 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.82 | 0.83 | 112 | PO4, CA |
| 2 | 95 | 0.78 | 0.98 | 30 | empty |
| 3 | 85 | 0.76 | 0.98 | 32 | empty |
| 4 | 88 | 0.47 | 0.81 | 19 | empty |
| 5 | 61 | 0.46 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–B · 604 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 450 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 277 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3V64 · Crystal Structure of agrin and LRP4 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9QYP1 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 4… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P25304 · AlphaFold monomer V2.0 prediction for agrin (P25304) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9QYP1
- Every structure of UniProt P25304
- Elsewhere: RCSB PDB 3V64 · PDBe 3V64 · UniProt Q9QYP1 · UniProt P25304
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