Research workbench
Structure of B-lymphotropic polyomavirus VP1 in complex with 3'- sialyllactose
Analyse Structure of B-lymphotropic polyomavirus VP1 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
- 4MBY
- Type
- protein
- Length
- 2,743 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- Ligands
- GAL, SIA, BGC, CA, CL
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Major capsid protein VP1 | protein | 277 | 4% helix, 40% strand | — |
| B, C, J | Major capsid protein VP1 | protein | 275 | 4% helix, 41% strand | — |
| D | Major capsid protein VP1 | protein | 274 | 4% helix, 40% strand | — |
| F | Major capsid protein VP1 | protein | 274 | 4% helix, 41% strand | — |
| G | Major capsid protein VP1 | protein | 270 | 4% helix, 41% strand | — |
| H | Major capsid protein VP1 | protein | 273 | 4% helix, 40% strand | — |
| I | Major capsid protein VP1 | protein | 273 | 4% helix, 41% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, B, C, D, E, G, H, I, J, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 9 copies · chains A, B, C, D, E, G, H, I, J, F
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains J, F
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, F, B, J, C, I, D, E, G, H
- 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 | 581 | 0.68 | 0.78 | 76 | EDO, IPA |
| 2 | 548 | 0.67 | 0.78 | 79 | EDO, IPA |
| 3 | 354 | 0.63 | 0.79 | 51 | EDO |
| 4 | 362 | 0.63 | 0.79 | 57 | EDO |
| 5 | 343 | 0.62 | 0.79 | 55 | EDO |
Interfaces
25 interfaces between chains.
- H–I · 2469 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2462 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 2461 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2457 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2455 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4MBY · Structure of B-Lymphotropic Polyomavirus VP1 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
- Elsewhere: RCSB PDB 4MBY · PDBe 4MBY
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