MolNFT v1 · #190697 · protein
Crystal structure of SARS-cov-2 N-ctd in complex with gmp
7XXK · Nucleoprotein: “Crystal structure of SARS-cov-2 N-ctd in complex with gmp”. X-ray diffraction, 7 ligands (5GP, GUN, GMP), 7 pockets (best druggability 0.70). MolNFT v1 #190697 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7XXK
- Type
- protein
- Length
- 648 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- 5GP, GUN, GMP, K, NA, CL, SCN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Nucleoprotein | protein | 109 | 40% helix, 22% strand | P0DTC9 |
| B | Nucleoprotein | protein | 107 | 41% helix, 21% strand | P0DTC9 |
| C, F | Nucleoprotein | protein | 107 | 38% helix, 21% strand | P0DTC9 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 3 copies · chains A, B, C, D
- GUN · Guanine · ligand · chains C, D, F
- GMP · Guanosine · ligand · chains E, F
- K · Potassium ion · metal · 9 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 2 copies · chains C, F
- CL · Chloride ion · ion · 13 copies · chains B, C, F, D, E, A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.70 | 0.81 | 64 | 5GP |
| 2 | 257 | 0.56 | 0.77 | 41 | GUN, CL |
| 3 | 171 | 0.55 | 0.80 | 25 | CL |
| 4 | 145 | 0.53 | 0.80 | 19 | K |
| 5 | 83 | 0.36 | 0.76 | 24 | GMP |
Interfaces
9 interfaces between chains.
- A–B · 2762 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2728 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2725 Ų buried · 44 hydrogen bonds · protein-protein
- C–F · 302 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7XXK · Crystal structure of SARS-CoV-2 N-CTD in complex with GMP · 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 P0DTC9
- Elsewhere: RCSB PDB 7XXK · PDBe 7XXK · UniProt P0DTC9
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