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The crystal structure of macrobrachium rosenbergii nodavirus P-domain
Analyse The crystal structure of macrobrachium rosenbergii nodavirus P-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKV
- Type
- protein
- Length
- 996 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q6XNL3
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, H | Capsid protein | protein | 124 | 2% helix, 58% strand | Q6XNL3 |
| B, D, E, G | Capsid protein | protein | 125 | 2% helix, 58% strand | Q6XNL3 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.66 | 0.76 | 65 | empty |
| 2 | 614 | 0.66 | 0.76 | 65 | empty |
| 3 | 117 | 0.46 | 0.79 | 19 | empty |
| 4 | 59 | 0.33 | 0.77 | 11 | empty |
| 5 | 52 | 0.32 | 0.78 | 11 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1484 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1479 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1474 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1466 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 680 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YKV · The crystal structure of Macrobrachium rosenbergii nodavirus P-domain · 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 Q6XNL3
- Elsewhere: RCSB PDB 5YKV · PDBe 5YKV · UniProt Q6XNL3
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