MolNFT v1 · #179168 · protein
Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by structure-guided high-resolution serology
7JXD · S2A4 antigen-binding (Fab) fragment: “Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by…”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #179168 on GenesisL1: 3D…
- PDB
- 7JXD
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2A4 antigen-binding (Fab) fragment
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S2A4 antigen-binding (Fab) fragment | protein | 210 | 6% helix, 52% strand | — |
| B, D | S2A4 antigen-binding (Fab) fragment | protein | 214 | 6% helix, 50% strand | — |
| C | S2A4 antigen-binding (Fab) fragment | protein | 220 | 5% helix, 49% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.65 | 0.75 | 72 | empty |
| 2 | 316 | 0.51 | 0.73 | 45 | empty |
| 3 | 219 | 0.50 | 0.75 | 26 | empty |
| 4 | 170 | 0.44 | 0.74 | 38 | empty |
| 5 | 65 | 0.39 | 0.80 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1966 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1781 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 193 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7JXD · Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding… · 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
- Elsewhere: RCSB PDB 7JXD · PDBe 7JXD
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