Research workbench
3A structure of lassa virus nucleoprotein in complex with ssrna
Analyse 3A structure of lassa virus nucleoprotein in complex with ssrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T5Q
- Type
- protein + RNA
- Length
- 1,850 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3'); RNA…
- UniProt
- Q5S585
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 306 | 55% helix, 7% strand | Q5S585 |
| C, F | RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3') | rna | 8 | — | — |
| B | Nucleoprotein | protein | 301 | 56% helix, 6% strand | Q5S585 |
| D | RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3') | rna | 7 | — | — |
| E | Nucleoprotein | protein | 301 | 56% helix, 7% strand | Q5S585 |
| G | Nucleoprotein | protein | 303 | 56% helix, 6% strand | Q5S585 |
| H, L | RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3') | rna | 6 | — | — |
| I | Nucleoprotein | protein | 302 | 57% helix, 7% strand | Q5S585 |
| J | RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3') | rna | 8 | — | — |
| K | Nucleoprotein | protein | 294 | 57% helix, 3% strand | Q5S585 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.84 | 0.96 | 28 | empty |
| 2 | 313 | 0.84 | 0.94 | 27 | empty |
| 3 | 332 | 0.84 | 0.94 | 34 | empty |
| 4 | 275 | 0.83 | 0.95 | 28 | empty |
| 5 | 347 | 0.82 | 0.92 | 35 | empty |
Interfaces
14 interfaces between chains.
- I–J · 1216 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–C · 1204 Ų buried · 37 hydrogen bonds · protein-nucleic
- E–F · 1179 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–D · 1105 Ų buried · 34 hydrogen bonds · protein-nucleic
- G–H · 1005 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 3T5Q · 3A structure of Lassa virus nucleoprotein in complex with ssRNA · 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 Q5S585
- Elsewhere: RCSB PDB 3T5Q · PDBe 3T5Q · UniProt Q5S585
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