MolNFT v1 · #188250 · protein + RNA
SARS-cov-2 endoribonuclease NSP15 bound to dsrna
7TJ2 · Uridylate-specific endoribonuclease NSP15: “SARS-cov-2 endoribonuclease NSP15 bound to dsrna”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #188250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TJ2
- Type
- protein + RNA
- Length
- 2,069 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease NSP15; RNA (31-mer)
- EC
- 4.6.1.-
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate-specific endoribonuclease NSP15 (EC 4.6.1.-) | protein | 348 | 21% helix, 30% strand | P0DTD1 |
| B, C, E, F | Uridylate-specific endoribonuclease NSP15 (EC 4.6.1.-) | protein | 347 | 22% helix, 28% strand | P0DTD1 |
| D | Uridylate-specific endoribonuclease NSP15 (EC 4.6.1.-) | protein | 271 | 16% helix, 32% strand | P0DTD1 |
| G | RNA (31-mer) | rna | 31 | — | — |
| H | RNA (31-mer) | rna | 31 | — | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.88 | 0.90 | 153 | empty |
| 2 | 756 | 0.76 | 0.81 | 62 | empty |
| 3 | 471 | 0.68 | 0.79 | 55 | empty |
| 4 | 442 | 0.68 | 0.79 | 56 | empty |
| 5 | 439 | 0.67 | 0.79 | 47 | empty |
Interfaces
22 interfaces between chains.
- G–H · 1439 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- A–C · 1264 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1249 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1248 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1240 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7TJ2 · SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA · 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 P0DTD1
- Elsewhere: RCSB PDB 7TJ2 · PDBe 7TJ2 · UniProt P0DTD1
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