MolNFT v1 · #179159 · protein
Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by structure-guided high-resolution serology
7JX3 · Light chain of Fab domain of monoclonal antibody S309: “Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.66).…
- PDB
- 7JX3
- Type
- protein
- Length
- 1,512 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab domain of monoclonal antibody S309; Heavy chain of Fab domain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Light chain of Fab domain of monoclonal antibody S309 | protein | 213 | 6% helix, 53% strand | — |
| A | Heavy chain of Fab domain of monoclonal antibody S309 | protein | 224 | 7% helix, 52% strand | — |
| D | Light chain of Fab domain of monoclonal antibody S2H14 | protein | 213 | 7% helix, 52% strand | — |
| C | Heavy chain of Fab domain of monoclonal antibody S2H14 | protein | 227 | 8% helix, 48% strand | — |
| L | Light chain of Fab domain of monoclonal antibody S304 | protein | 215 | 6% helix, 52% strand | — |
| H | Heavy chain of Fab domain of monoclonal antibody S304 | protein | 222 | 9% helix, 55% strand | — |
| R | Spike protein S1 | protein | 198 | 16% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B, A, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.66 | 0.74 | 61 | empty |
| 2 | 71 | 0.56 | 0.88 | 21 | empty |
| 3 | 228 | 0.56 | 0.78 | 36 | empty |
| 4 | 239 | 0.52 | 0.76 | 34 | empty |
| 5 | 59 | 0.52 | 0.88 | 23 | empty |
Interfaces
9 interfaces between chains.
- L–H · 2130 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 1827 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 1666 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 687 Ų buried · 12 hydrogen bonds · protein-protein
- H–R · 553 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JX3 · Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding… · the same entry in another collection · chain R against R, 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 P0DTC2
- Elsewhere: RCSB PDB 7JX3 · PDBe 7JX3 · UniProt P0DTC2
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