Research workbench
Cryo-EM structure of veev vlp-LDLRAD3-D1 complex at the 5-fold axes
Analyse Cryo-EM structure of veev vlp-LDLRAD3-D1 complex at the 5-fold axes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FFN
- Type
- protein
- Length
- 1,112 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Assembly protein E3; Low-density lipoprotein receptor class a…
- EC
- 3.4.21.90
- UniProt
- P05674, Q86YD5
- Ligands
- CA
- Pockets
- 14 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Capsid protein (EC 3.4.21.90) | protein | 163 | 10% helix, 42% strand | P05674 |
| L | Assembly protein E3 | protein | 50 | 38% helix, 12% strand | P05674 |
| M | Low-density lipoprotein receptor class a domain-containing protein 3 | protein | 38 | 16% helix, 16% strand | Q86YD5 |
| N | Spike glycoprotein E2 | protein | 419 | 15% helix, 37% strand | P05674 |
| O | Spike glycoprotein E1 | protein | 442 | 12% helix, 40% strand | P05674 |
Ligands and binding sites
- CA · Calcium ion · metal · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.74 | 0.78 | 73 | empty |
| 2 | 393 | 0.68 | 0.80 | 39 | empty |
| 3 | 515 | 0.65 | 0.77 | 41 | empty |
| 4 | 409 | 0.61 | 0.77 | 49 | empty |
| 5 | 135 | 0.55 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- N–O · 3604 Ų buried · 32 hydrogen bonds · protein-protein
- L–N · 808 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 579 Ų buried · 3 hydrogen bonds · protein-protein
- K–N · 549 Ų buried · 4 hydrogen bonds · protein-protein
- K–O · 346 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7FFN · Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes · the same entry in another collection · chain K against K, TM-score 1.00
- Q86YD5 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor class a… · a predicted model of the same protein · chain M against A, TM-score 0.77
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 P05674
- Every structure of UniProt Q86YD5
- Elsewhere: RCSB PDB 7FFN · PDBe 7FFN · UniProt P05674 · UniProt Q86YD5
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