Research workbench
Crystal structure of 2019-ncov nucleocapsid N-terminal domain (ntd) protein
Analyse Crystal structure of 2019-ncov nucleocapsid N-terminal domain (ntd) protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CDZ
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 128 | 2% helix, 23% strand | P0DTC9 |
| B | Nucleoprotein | protein | 127 | 2% helix, 24% strand | P0DTC9 |
| C | Nucleoprotein | protein | 126 | 5% helix, 25% strand | P0DTC9 |
| D | Nucleoprotein | protein | 127 | 2% helix, 24% strand | P0DTC9 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.85 | 0.86 | 79 | empty |
| 2 | 398 | 0.75 | 0.85 | 39 | empty |
| 3 | 356 | 0.73 | 0.84 | 39 | empty |
| 4 | 178 | 0.47 | 0.76 | 22 | empty |
| 5 | 139 | 0.44 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 675 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CDZ · Crystal structure of 2019-nCoV nucleocapsid N-terminal domain (NTD) protein · 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 7CDZ · PDBe 7CDZ · UniProt P0DTC9
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