Research workbench
Crystal structure of the GP2 core domain from the california academy of science virus
Analyse Crystal structure of the GP2 core domain from the california academy of science… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N21
- Type
- protein
- Length
- 738 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP2 ectodomain
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | GP2 ectodomain | protein | 123 | 82% helix, 0% strand | — |
| C, F | GP2 ectodomain | protein | 124 | 84% helix, 0% strand | — |
| E | GP2 ectodomain | protein | 121 | 83% helix, 0% strand | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.82 | 0.83 | 107 | MPD |
| 2 | 91 | 0.78 | 0.99 | 22 | MPD |
| 3 | 90 | 0.78 | 0.99 | 21 | MPD |
| 4 | 206 | 0.55 | 0.79 | 30 | empty |
| 5 | 53 | 0.34 | 0.79 | 14 | empty |
Interfaces
11 interfaces between chains.
- B–C · 2284 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2259 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 2247 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2212 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4N21 · Crystal structure of the GP2 Core Domain from the California Academy of Science Virus · 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 4N21 · PDBe 4N21
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