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Crystal structure of human Fab S24-1379 in the complex with the N- teminal domain of nucleocapsid protein from SARS cov-2
Analyse Crystal structure of human Fab S24-1379 in the complex with the N- teminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7STS
- Type
- protein
- Length
- 1,074 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab S24-1379, heavy chain; Fab S24-1379, light chain; Nucleoprotein
- UniProt
- P0DTC9
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab S24-1379, heavy chain | protein | 204 | 3% helix, 54% strand | — |
| B, L | Fab S24-1379, light chain | protein | 212 | 7% helix, 50% strand | — |
| C | Nucleoprotein | protein | 111 | 3% helix, 21% strand | P0DTC9 |
| D | Nucleoprotein | protein | 125 | 0% helix, 24% strand | P0DTC9 |
| H | Fab S24-1379, heavy chain | protein | 210 | 4% helix, 52% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.80 | 0.82 | 111 | empty |
| 2 | 488 | 0.59 | 0.74 | 58 | empty |
| 3 | 447 | 0.57 | 0.74 | 44 | empty |
| 4 | 135 | 0.53 | 0.80 | 22 | empty |
| 5 | 82 | 0.41 | 0.79 | 19 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1718 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1654 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 283 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7STS · Crystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of… · 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 7STS · PDBe 7STS · UniProt P0DTC9
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