MolNFT v1 · #177192 · protein
ECHOVIRUS3 full particle in complex with 5G3 Fab
7EAK · Capsid protein VP1: “ECHOVIRUS3 full particle in complex with 5G3 Fab”. Electron microscopy, 2 ligands (SPH, MYR), 12 pockets (best druggability 0.80). MolNFT v1 #177192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EAK
- Type
- protein
- Length
- 1,056 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; Heavy…
- UniProt
- A0A6M4MJE3
- Ligands
- SPH, MYR
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 283 | 11% helix, 31% strand | A0A6M4MJE3 |
| B | Capsid protein VP2 | protein | 251 | 7% helix, 32% strand | A0A6M4MJE3 |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 30% strand | A0A6M4MJE3 |
| D | Capsid protein VP4 | protein | 57 | 12% helix, 16% strand | A0A6M4MJE3 |
| F | Heavy chain of 5G3 Fab | protein | 112 | 5% helix, 44% strand | — |
| L | Light chain of 5G3 Fab | protein | 115 | 0% helix, 43% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.80 | 0.88 | 62 | SPH |
| 2 | 150 | 0.51 | 0.79 | 25 | empty |
| 3 | 128 | 0.50 | 0.80 | 19 | empty |
| 4 | 118 | 0.49 | 0.80 | 24 | empty |
| 5 | 187 | 0.46 | 0.75 | 24 | empty |
Interfaces
11 interfaces between chains.
- A–C · 4453 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2135 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1602 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1191 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent, 1 lipid (disulfide, covalent ligand, myristoylation).
Compared structures
- 7EAK · Echovirus3 full particle in complex with 5G3 fab · 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 A0A6M4MJE3
- Elsewhere: RCSB PDB 7EAK · PDBe 7EAK · UniProt A0A6M4MJE3
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