Research workbench
Atomic cryoem structure of a nonenveloped virus suggests how membrane penetration protein is primed for cell entry
Analyse Atomic cryoem structure of a nonenveloped virus suggests how membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IYL
- Type
- protein
- Length
- 10,728 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid VP4; Core protein VP6; VP1; VP3
- UniProt
- Q8JU67, Q8JU64, Q9E3W0, Q9E3V8
- Ligands
- MYR
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 6 distinct chains · 30% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S | Outer capsid VP4 | protein | 41 | 10% helix, 7% strand | Q8JU67 |
| B, D, F, H, J, L, N, P, R, T | Outer capsid VP4 | protein | 604 | 37% helix, 13% strand | Q8JU67 |
| U, V | Core protein VP6 | protein | 411 | 33% helix, 8% strand | Q8JU64 |
| W | VP1 | protein | 1284 | 23% helix, 21% strand | Q9E3W0 |
| X | VP3 | protein | 1018 | 33% helix, 13% strand | Q9E3V8 |
| Y | VP3 | protein | 1154 | 31% helix, 10% strand | Q9E3V8 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.89 | 0.91 | 141 | empty |
| 2 | 941 | 0.88 | 0.90 | 144 | empty |
| 3 | 412 | 0.86 | 0.94 | 71 | empty |
| 4 | 1031 | 0.86 | 0.87 | 95 | empty |
| 5 | 1034 | 0.86 | 0.87 | 96 | empty |
Interfaces
76 interfaces between chains.
- D–H · 4440 Ų buried · 48 hydrogen bonds · protein-protein
- P–T · 4438 Ų buried · 50 hydrogen bonds · protein-protein
- J–N · 4436 Ų buried · 48 hydrogen bonds · protein-protein
- D–F · 4432 Ų buried · 48 hydrogen bonds · protein-protein
- R–T · 4428 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 lipid, 1 disulfide (myristoylation, disulfide).
Compared structures
- 3IYL · Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein… · the same entry in another collection · chain P against P, 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 Q8JU67
- Every structure of UniProt Q8JU64
- Every structure of UniProt Q9E3W0
- Every structure of UniProt Q9E3V8
- Elsewhere: RCSB PDB 3IYL · PDBe 3IYL · UniProt Q8JU67 · UniProt Q8JU64 · UniProt Q9E3W0 · UniProt Q9E3V8
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