Research workbench
Crystal structure of human Fab S24-1564 in the complex with the N- terminal domain of nucleocapsid protein from SARS cov-2
Analyse Crystal structure of human Fab S24-1564 in the complex with the N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N3D
- Type
- protein
- Length
- 546 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S24-1564 Fab heavy chain; S24-1564 Fab light chain; Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S24-1564 Fab heavy chain | protein | 223 | 8% helix, 55% strand | — |
| L | S24-1564 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| C | Nucleoprotein | protein | 110 | 3% helix, 22% strand | P0DTC9 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains H, L, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains H, L, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.68 | 0.75 | 67 | EDO |
| 2 | 180 | 0.48 | 0.76 | 26 | empty |
| 3 | 95 | 0.44 | 0.79 | 22 | EDO |
| 4 | 106 | 0.36 | 0.73 | 18 | empty |
| 5 | 52 | 0.26 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1855 Ų buried · 19 hydrogen bonds · protein-protein
- H–C · 621 Ų buried · 7 hydrogen bonds · protein-protein
- L–C · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7N3D · Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of… · the same entry in another collection · chain H against H, 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 7N3D · PDBe 7N3D · UniProt P0DTC9
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