MolNFT v1 · #186622 · protein
Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scfv 2D9, an astrovirus-neutralizing antibody, at 2.65-a resolution
7RK2 · Capsid protein VP25: “Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scfv 2D9, an…”. X-ray diffraction, 9 pockets (best druggability 0.66). MolNFT v1 #186622 on GenesisL1: 3D structure, binding…
- PDB
- 7RK2
- Type
- protein
- Length
- 883 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP25; Scfv 2D9
- UniProt
- Q9IFX1
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP25 | protein | 217 | 1% helix, 48% strand | Q9IFX1 |
| B | Capsid protein VP25 | protein | 218 | 1% helix, 47% strand | Q9IFX1 |
| C, D | Scfv 2D9 | protein | 224 | 3% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.66 | 0.81 | 42 | empty |
| 2 | 237 | 0.50 | 0.75 | 34 | empty |
| 3 | 226 | 0.49 | 0.75 | 39 | empty |
| 4 | 54 | 0.39 | 0.81 | 20 | empty |
| 5 | 52 | 0.38 | 0.81 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1832 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 890 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 870 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 98 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RK2 · Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv… · 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 Q9IFX1
- Elsewhere: RCSB PDB 7RK2 · PDBe 7RK2 · UniProt Q9IFX1
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