Research workbench
Crystal structure of human Fab S24-202 in the complex with the N- terminal domain of nucleocapsid protein from SARS cov-2
Analyse Crystal structure of human Fab S24-202 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
- 7N3C
- Type
- protein
- Length
- 570 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S24-202 Fab heavy chain; S24-202 Fab light chain; Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- IOD, PO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S24-202 Fab heavy chain | protein | 226 | 8% helix, 52% strand | — |
| L | S24-202 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| C | Nucleoprotein | protein | 130 | 8% helix, 25% strand | P0DTC9 |
Ligands and binding sites
- IOD · Iodide ion · ion · 12 copies · chains H, L, C
- PO4 · Phosphate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 9 copies · chains H, L, C
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 | 175 | 0.58 | 0.81 | 26 | IOD, EDO |
| 2 | 70 | 0.56 | 0.88 | 20 | IOD |
| 3 | 382 | 0.55 | 0.74 | 47 | empty |
| 4 | 222 | 0.52 | 0.76 | 32 | IOD |
| 5 | 145 | 0.42 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1791 Ų buried · 11 hydrogen bonds · protein-protein
- H–C · 491 Ų buried · 9 hydrogen bonds · protein-protein
- L–C · 301 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7N3C · Crystal Structure of Human Fab S24-202 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 7N3C · PDBe 7N3C · UniProt P0DTC9
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