MolNFT v1 · #103714 · protein
Structure of human polyomavirus 9 VP1 pentamer in complex with N- glycolylneuraminic acid containing 3'-sialyllactosamine
4POT: “Structure of human polyomavirus 9 VP1 pentamer in complex with N- glycolylneuraminic acid containing…”. X-ray diffraction, 4 ligands (NAG, GAL, NGC), 20 pockets (best druggability 0.64). MolNFT v1 #103714 on GenesisL1: 3D structure…
- PDB
- 4POT
- Type
- protein
- Length
- 2,700 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- E9NQ90
- Ligands
- NAG, GAL, NGC, CA
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | VP1 | protein | 269 | 5% helix, 41% strand | E9NQ90 |
| B, D, G, H | VP1 | protein | 270 | 5% helix, 40% strand | E9NQ90 |
| E, I | VP1 | protein | 269 | 5% helix, 39% strand | E9NQ90 |
| F, J | VP1 | protein | 272 | 5% helix, 39% strand | E9NQ90 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, C, D, E, A, G, H, I, J, F
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · 10 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 · 29 copies · chains A, B, C, G, D, F, E, H, I, J
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.64 | 0.82 | 41 | EDO |
| 2 | 237 | 0.63 | 0.82 | 33 | empty |
| 3 | 435 | 0.62 | 0.77 | 59 | EDO, IPA |
| 4 | 440 | 0.62 | 0.77 | 57 | EDO, IPA |
| 5 | 218 | 0.61 | 0.81 | 40 | empty |
Interfaces
15 interfaces between chains.
- G–H · 2197 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2189 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 2188 Ų buried · 36 hydrogen bonds · protein-protein
- H–I · 2187 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2187 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4POT · Structure of Human Polyomavirus 9 VP1 pentamer in complex with N-glycolylneuraminic acid… · 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 4POT · PDBe 4POT · UniProt E9NQ90
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