MolNFT v1 · #183220 · protein
Crystal structure of the SARS-cov-2 helicase apo form
7NIO · SARS-cov-2 helicase NSP13: “Crystal structure of the SARS-cov-2 helicase apo form”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.77). MolNFT v1 #183220 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7NIO
- Type
- protein
- Length
- 1,175 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS-cov-2 helicase NSP13
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARS-cov-2 helicase NSP13 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 590 | 28% helix, 24% strand | P0DTD1 |
| E | SARS-cov-2 helicase NSP13 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 585 | 30% helix, 24% strand | P0DTD1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, E
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 | 546 | 0.77 | 0.84 | 46 | empty |
| 2 | 489 | 0.77 | 0.85 | 42 | empty |
| 3 | 381 | 0.75 | 0.85 | 39 | empty |
| 4 | 712 | 0.74 | 0.80 | 55 | empty |
| 5 | 93 | 0.58 | 0.87 | 28 | empty |
Interfaces
1 interface between chains.
- A–E · 731 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7NIO · Crystal structure of the SARS-CoV-2 helicase APO form · 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 7NIO · PDBe 7NIO · UniProt P0DTD1
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