MolNFT v1 · #183520 · protein + RNA
Cryoem structure of the nipah virus nucleocapsid spiral clam-shaped assembly
7NT6 · Nucleoprotein: “Cryoem structure of the nipah virus nucleocapsid spiral clam-shaped assembly”. Electron microscopy, 20 pockets (best druggability 0.76). MolNFT v1 #183520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NT6
- Type
- protein + RNA
- Length
- 5,672 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; RNA (48-mer); RNA (42-mer)
- UniProt
- Q9IK92
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 16 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 330 | 62% helix, 5% strand | Q9IK92 |
| B | Nucleoprotein | protein | 361 | 63% helix, 4% strand | Q9IK92 |
| C, D | Nucleoprotein | protein | 368 | 61% helix, 5% strand | Q9IK92 |
| E | Nucleoprotein | protein | 382 | 58% helix, 4% strand | Q9IK92 |
| F | Nucleoprotein | protein | 388 | 59% helix, 5% strand | Q9IK92 |
| G | Nucleoprotein | protein | 363 | 60% helix, 4% strand | Q9IK92 |
| H | Nucleoprotein | protein | 381 | 62% helix, 5% strand | Q9IK92 |
| I | Nucleoprotein | protein | 388 | 60% helix, 5% strand | Q9IK92 |
| J | Nucleoprotein | protein | 393 | 57% helix, 5% strand | Q9IK92 |
| K | Nucleoprotein | protein | 390 | 59% helix, 5% strand | Q9IK92 |
| L | Nucleoprotein | protein | 375 | 60% helix, 5% strand | Q9IK92 |
| M | Nucleoprotein | protein | 366 | 60% helix, 5% strand | Q9IK92 |
| N | Nucleoprotein | protein | 365 | 60% helix, 5% strand | Q9IK92 |
| O | Nucleoprotein | protein | 364 | 60% helix, 5% strand | Q9IK92 |
| X | RNA (48-mer) | rna | 48 | — | — |
| Z | RNA (42-mer) | rna | 42 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.76 | 0.80 | 162 | empty |
| 2 | 720 | 0.72 | 0.79 | 107 | empty |
| 3 | 624 | 0.71 | 0.80 | 90 | empty |
| 4 | 551 | 0.70 | 0.80 | 96 | empty |
| 5 | 526 | 0.69 | 0.80 | 80 | empty |
Interfaces
34 interfaces between chains.
- I–J · 573 Ų buried · 4 hydrogen bonds · protein-protein
- H–I · 562 Ų buried · 4 hydrogen bonds · protein-protein
- J–K · 550 Ų buried · 4 hydrogen bonds · protein-protein
- F–Z · 509 Ų buried · 4 hydrogen bonds · protein-nucleic
- N–X · 509 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7NT6 · CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly · 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 Q9IK92
- Elsewhere: RCSB PDB 7NT6 · PDBe 7NT6 · UniProt Q9IK92
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