MolNFT v1 · #183353 · protein
Crystal structure of the SARS-cov-2 helicase in complex with AMP-pnp
7NN0 · SARS-cov-2 helicase NSP13: “Crystal structure of the SARS-cov-2 helicase in complex with AMP-pnp”. X-ray diffraction, 3 ligands (ANP, ZN, MG), 20 pockets (best druggability 0.78). MolNFT v1 #183353 on GenesisL1: 3D structure…
- PDB
- 7NN0
- Type
- protein
- Length
- 2,348 residues
- Chains
- 4
- 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
- ANP, ZN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% 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 | 588 | 28% helix, 26% strand | P0DTD1 |
| B | 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, 25% strand | P0DTD1 |
| C, D | 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 | 28% helix, 25% strand | P0DTD1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.78 | 0.87 | 45 | empty |
| 2 | 699 | 0.77 | 0.82 | 71 | empty |
| 3 | 500 | 0.75 | 0.83 | 44 | empty |
| 4 | 306 | 0.74 | 0.86 | 51 | empty |
| 5 | 560 | 0.72 | 0.80 | 54 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1752 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 652 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 285 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 193 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7NN0 · Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP · 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 7NN0 · PDBe 7NN0 · UniProt P0DTD1
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