MolNFT v1 · #183787 · protein
Crystal structure of SARS-cov-2 N-ctd in complex with GTP (II)
7O36 · Nucleoprotein: “Crystal structure of SARS-cov-2 N-ctd in complex with GTP (II)”. X-ray diffraction, 1 ligand (GTP), 4 pockets (best druggability 0.56). MolNFT v1 #183787 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7O36
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- GTP
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 112 | 37% helix, 21% strand | P0DTC9 |
| B | Nucleoprotein | protein | 109 | 40% helix, 18% strand | P0DTC9 |
| C | Nucleoprotein | protein | 113 | 36% helix, 20% strand | P0DTC9 |
| D | Nucleoprotein | protein | 111 | 40% helix, 18% strand | P0DTC9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.56 | 0.76 | 39 | GTP |
| 2 | 137 | 0.45 | 0.76 | 23 | empty |
| 3 | 75 | 0.33 | 0.75 | 18 | empty |
| 4 | 53 | 0.30 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2705 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2701 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 424 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7O36 · Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (II) · 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 7O36 · PDBe 7O36 · UniProt P0DTC9
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