Research workbench
Cryo-EM structure of human POLIOVIRUS(SEROTYPE 1)COMPLEXED with three domain CD155
Analyse Cryo-EM structure of human POLIOVIRUS(SEROTYPE 1)COMPLEXED with three domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DGI
- Type
- protein
- Length
- 1,154 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus receptor; VP1; VP2; VP3; VP4
- UniProt
- P15151, P03300
- Ligands
- MYR
- Pockets
- 3 · best druggability 0.32
Structure
electron microscopy · 5 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Poliovirus receptor | protein | 301 | 0% helix, 0% strand | P15151 |
| 1 | VP1 | protein | 288 | 0% helix, 0% strand | P03300 |
| 2 | VP2 | protein | 268 | 0% helix, 0% strand | P03300 |
| 3 | VP3 | protein | 235 | 0% helix, 0% strand | P03300 |
| 4 | VP4 | protein | 62 | 0% helix, 0% strand | — |
Ligands and binding sites
- MYR · Myristic acid · ion · chains 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.32 | 0.72 | 22 | empty |
| 2 | 54 | 0.30 | 0.74 | 19 | empty |
| 3 | 55 | 0.27 | 0.72 | 18 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 559 Ų buried · 0 hydrogen bonds · protein-protein
- 1–2 · 426 Ų buried · 0 hydrogen bonds · protein-protein
- 1–4 · 291 Ų buried · 0 hydrogen bonds · protein-protein
- 2–3 · 242 Ų buried · 0 hydrogen bonds · protein-protein
- 2–4 · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1DGI · Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 · the same entry in another collection · chain 2 against 2, TM-score 1.00
- P15151 · AlphaFold monomer V2.0 prediction for poliovirus receptor (P15151) · a predicted model of the same protein · chain R against A, TM-score 0.69
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 P15151
- Every structure of UniProt P03300
- Elsewhere: RCSB PDB 1DGI · PDBe 1DGI · UniProt P15151 · UniProt P03300
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