Research workbench
Structure of human polyomavirus 9 VP1 pentamer in complex with 3'- sialyllactose
Analyse Structure of human polyomavirus 9 VP1 pentamer in complex with 3'- sialyllactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4POR
- Type
- protein
- Length
- 2,698 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- E9NQ90
- Ligands
- BGC, GAL, SIA, CA
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, H | VP1 | protein | 270 | 5% helix, 39% strand | E9NQ90 |
| C, E | VP1 | protein | 269 | 5% helix, 39% strand | E9NQ90 |
| F | VP1 | protein | 272 | 5% helix, 39% strand | E9NQ90 |
| G | VP1 | protein | 266 | 5% helix, 40% strand | E9NQ90 |
| I | VP1 | protein | 269 | 5% helix, 39% strand | E9NQ90 |
| J | VP1 | protein | 273 | 5% helix, 38% strand | E9NQ90 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains B, C, E, A, G, H, I, J, F
- GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, B, C, D, E, F, G, H, I, J
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 9 copies · chains A, B, C, D, E, F, G, H, I, J
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, B, E, C, D, F, J, G, H, I
- IPA · Isopropyl alcohol · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.64 | 0.81 | 45 | empty |
| 2 | 287 | 0.64 | 0.81 | 42 | empty |
| 3 | 286 | 0.64 | 0.81 | 41 | empty |
| 4 | 577 | 0.64 | 0.75 | 85 | EDO, IPA |
| 5 | 196 | 0.62 | 0.83 | 33 | EDO |
Interfaces
15 interfaces between chains.
- H–I · 2202 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 2200 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 2198 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2193 Ų buried · 38 hydrogen bonds · protein-protein
- F–J · 2192 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4POR · Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose · 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 E9NQ90
- Elsewhere: RCSB PDB 4POR · PDBe 4POR · UniProt E9NQ90
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