MolNFT v1 · #177898 · protein
The N-terminal crystal structure of SARS-cov-2 NSP2
7EXM · Non-structural protein 2: “The N-terminal crystal structure of SARS-cov-2 NSP2”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.77). MolNFT v1 #177898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EXM
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 2
- UniProt
- P0DTC1
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 2 | protein | 278 | 22% helix, 28% strand | P0DTC1 |
| B | Non-structural protein 2 | protein | 273 | 20% helix, 29% strand | P0DTC1 |
| C | Non-structural protein 2 | protein | 274 | 20% helix, 31% strand | P0DTC1 |
| D | Non-structural protein 2 | protein | 274 | 23% helix, 31% strand | P0DTC1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.77 | 0.81 | 77 | empty |
| 2 | 817 | 0.76 | 0.80 | 56 | empty |
| 3 | 813 | 0.75 | 0.80 | 65 | empty |
| 4 | 379 | 0.59 | 0.76 | 37 | GOL |
| 5 | 320 | 0.56 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- B–D · 699 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 458 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 274 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 248 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EXM · The N-terminal crystal structure of SARS-CoV-2 NSP2 · 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 P0DTC1
- Elsewhere: RCSB PDB 7EXM · PDBe 7EXM · UniProt P0DTC1
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