MolNFT v1 · #31956 · protein + RNA
The refined three-dimensional structure of an insect virus at 2.8 ångströms resolution
2BBV · RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3'): “The refined three-dimensional structure of an insect virus at 2.8 ångströms resolution”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.84). MolNFT v1 #31956 on…
- PDB
- 2BBV
- Type
- protein + RNA
- Length
- 995 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3'); Protein (black beetle virus capsid protein)
- UniProt
- P04329
- Ligands
- CA
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | rna | 10 | — | — |
| A, B | Protein (black beetle virus capsid protein) | protein | 308 | 16% helix, 38% strand | P04329 |
| D, E, F | Protein (black beetle virus capsid protein) | protein | 16 | 63% helix, 0% strand | P04329 |
| C | Protein (black beetle virus capsid protein) | protein | 321 | 15% helix, 37% strand | P04329 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.84 | 0.85 | 61 | CA |
| 2 | 294 | 0.76 | 0.88 | 29 | empty |
| 3 | 296 | 0.76 | 0.88 | 28 | empty |
| 4 | 290 | 0.75 | 0.88 | 30 | empty |
| 5 | 260 | 0.74 | 0.88 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1749 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1739 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1725 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 748 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 722 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2BBV · The refined three-dimensional structure of an insect virus at 2.8 ångströms resolution · the same entry in another collection · chain N against N, 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 P04329
- Elsewhere: RCSB PDB 2BBV · PDBe 2BBV · UniProt P04329
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