Research workbench
Crystal structure of the APOER2 ectodomain in complex with the reelin R56 fragment
Analyse Crystal structure of the APOER2 ectodomain in complex with the reelin R56… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B4X
- Type
- protein
- Length
- 2,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reelin; Low density lipoprotein receptor-related protein 8, apolipoprotein E receptor…
- EC
- 3.4.21.-
- UniProt
- Q60841, D3DQ39
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reelin (EC 3.4.21.-) | protein | 710 | 3% helix, 40% strand | Q60841 |
| B, D | Low density lipoprotein receptor-related protein 8, apolipoprotein E receptor, isoform CRA_E | protein | 479 | 6% helix, 40% strand | D3DQ39 |
| C | Reelin (EC 3.4.21.-) | protein | 709 | 3% helix, 39% strand | Q60841 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · 16 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.84 | 0.97 | 44 | empty |
| 2 | 242 | 0.83 | 0.96 | 46 | empty |
| 3 | 881 | 0.82 | 0.84 | 101 | empty |
| 4 | 983 | 0.79 | 0.81 | 94 | empty |
| 5 | 905 | 0.77 | 0.80 | 69 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1337 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1290 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1271 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 345 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide, 20 modified, 5 glycan (disulfide, engineered, N-glycosylation).
Compared structures
- 5B4X · Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment · 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 Q60841
- Every structure of UniProt D3DQ39
- Elsewhere: RCSB PDB 5B4X · PDBe 5B4X · UniProt Q60841 · UniProt D3DQ39
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