MolNFT v1 · #114190 · protein
Crystal structure of the APOER2 ectodomain in complex with the reelin R56 fragment
5B4X: “Crystal structure of the APOER2 ectodomain in complex with the reelin R56 fragment”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.84). MolNFT v1 #114190 on GenesisL1: 3D structure, binding sites and…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.