Research workbench
Feline calicivirus strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule a - leading to assembly of a portal structure at a unique three-fold axis.
Analyse Feline calicivirus strain F9 bound to a soluble ectodomain fragment of feline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GSI
- Type
- protein
- Length
- 3,277 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Junctional adhesion molecule a; VP2
- UniProt
- P27406, Q2WGK2, P28711
- Ligands
- K
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 10% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Capsid protein | protein | 534 | 7% helix, 27% strand | P27406 |
| B | Capsid protein | protein | 530 | 5% helix, 25% strand | P27406 |
| E | Junctional adhesion molecule a | protein | 201 | 3% helix, 39% strand | Q2WGK2 |
| F | Junctional adhesion molecule a | protein | 202 | 1% helix, 40% strand | Q2WGK2 |
| G | Junctional adhesion molecule a | protein | 200 | 3% helix, 42% strand | Q2WGK2 |
| H | Junctional adhesion molecule a | protein | 200 | 3% helix, 40% strand | Q2WGK2 |
| I, K | VP2 | protein | 82 | 66% helix, 0% strand | P28711 |
| J, L | VP2 | protein | 89 | 72% helix, 0% strand | P28711 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.83 | 0.88 | 73 | empty |
| 2 | 769 | 0.82 | 0.85 | 99 | empty |
| 3 | 1019 | 0.82 | 0.83 | 123 | empty |
| 4 | 676 | 0.80 | 0.85 | 70 | empty |
| 5 | 615 | 0.77 | 0.83 | 58 | empty |
Interfaces
31 interfaces between chains.
- C–D · 5094 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 4959 Ų buried · 52 hydrogen bonds · protein-protein
- K–L · 1568 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1527 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1434 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6GSI · Feline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional… · the same entry in another collection · chain L against L, 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 P27406
- Every structure of UniProt Q2WGK2
- Every structure of UniProt P28711
- Elsewhere: RCSB PDB 6GSI · PDBe 6GSI · UniProt P27406 · UniProt Q2WGK2 · UniProt P28711
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