MolNFT v1 · #144856 · protein
Crystal structure of the murine norovirus VP1 P domain in complex with the CD300LF receptor
6C6Q · Capsid protein VP1: “Crystal structure of the murine norovirus VP1 P domain in complex with the CD300LF receptor”. X-ray diffraction, 2 ligands (MG, CL), 8 pockets (best druggability 0.81). MolNFT v1 #144856 on GenesisL1: 3D…
- PDB
- 6C6Q
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; CMRF35-like molecule 1
- UniProt
- Q80J94, Q6SJQ7
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein VP1 | protein | 303 | 5% helix, 40% strand | Q80J94 |
| D | CMRF35-like molecule 1 | protein | 109 | 8% helix, 50% strand | Q6SJQ7 |
| F | CMRF35-like molecule 1 | protein | 113 | 8% helix, 49% strand | Q6SJQ7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, D, F
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.81 | 0.97 | 34 | EDO |
| 2 | 252 | 0.61 | 0.80 | 34 | CL, EDO |
| 3 | 267 | 0.59 | 0.79 | 33 | CL |
| 4 | 212 | 0.53 | 0.77 | 35 | EDO |
| 5 | 213 | 0.52 | 0.77 | 35 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1944 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 690 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6C6Q · Crystal Structure of the Murine Norovirus VP1 P Domain in complex with the CD300lf… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6SJQ7 · AlphaFold monomer V2.0 prediction for CMRF35-like molecule 1 (Q6SJQ7) · a predicted model of the same protein · chain D 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 Q80J94
- Every structure of UniProt Q6SJQ7
- Elsewhere: RCSB PDB 6C6Q · PDBe 6C6Q · UniProt Q80J94 · UniProt Q6SJQ7
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