MolNFT v1 · #96184 · protein
S268F variant of jc polyomavirus major capsid protein VP1 in complex with lstc
4JCF: “S268F variant of jc polyomavirus major capsid protein VP1 in complex with lstc”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 12 pockets (best druggability 0.60). MolNFT v1 #96184 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JCF
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Ligands
- NAG, GAL, SIA
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Major capsid protein VP1 | protein | 256 | 8% helix, 41% strand | P03089 |
| A | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| B | Major capsid protein VP1 | protein | 259 | 8% helix, 42% strand | P03089 |
| D, E | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C, D
- GAL · beta-D-galactopyranose · sugar · chains C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains C, D
- GOL · Glycerol · additive · 5 copies · chains C, B, A, E, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.60 | 0.76 | 62 | empty |
| 2 | 321 | 0.51 | 0.74 | 35 | empty |
| 3 | 229 | 0.50 | 0.75 | 29 | empty |
| 4 | 211 | 0.49 | 0.76 | 30 | empty |
| 5 | 159 | 0.49 | 0.78 | 35 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2357 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2340 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2331 Ų buried · 46 hydrogen bonds · protein-protein
- C–B · 2316 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 2308 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 4JCF · S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc · the same entry in another collection · chain C against C, 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 P03089
- Elsewhere: RCSB PDB 4JCF · PDBe 4JCF · UniProt P03089
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