MolNFT v1 · #155517 · protein
Cryo-EM structure of full echovirus 11 particle at pH 5.5
6LA4 · Capsid protein VP1: “Cryo-EM structure of full echovirus 11 particle at pH 5.5”. Electron microscopy, 1 ligand (SPH), 13 pockets (best druggability 0.78). MolNFT v1 #155517 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LA4
- Type
- protein
- Length
- 833 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- Ligands
- SPH
- Pockets
- 13 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 285 | 9% helix, 32% strand | — |
| B | Capsid protein VP2 | protein | 251 | 10% helix, 38% strand | — |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 30% strand | — |
| D | Capsid protein VP4 | protein | 59 | 12% helix, 17% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.78 | 0.84 | 83 | SPH |
| 2 | 50 | 0.70 | 0.98 | 16 | empty |
| 3 | 78 | 0.53 | 0.86 | 28 | empty |
| 4 | 129 | 0.52 | 0.81 | 30 | empty |
| 5 | 178 | 0.51 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4470 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 2100 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1485 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 924 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LA4 · Cryo-EM structure of full echovirus 11 particle at pH 5.5 · 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
- Elsewhere: RCSB PDB 6LA4 · PDBe 6LA4
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