Research workbench
Crystal structure of the 76E1 Fab in complex with a SARS-cov-2 spike peptide
Analyse Crystal structure of the 76E1 Fab in complex with a SARS-cov-2 spike peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X9E
- Type
- protein
- Length
- 871 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 76E1 Fab heavy chain; 76E1 Fab light chain; Spike peptide
- UniProt
- P0DTC2
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 76E1 Fab heavy chain | protein | 211 | 8% helix, 53% strand | — |
| B | 76E1 Fab light chain | protein | 211 | 6% helix, 49% strand | — |
| C | 76E1 Fab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| D | 76E1 Fab light chain | protein | 210 | 7% helix, 51% strand | — |
| E | Spike peptide | protein | 13 | 69% helix, 0% strand | P0DTC2 |
| F | Spike peptide | protein | 15 | 60% helix, 0% strand | P0DTC2 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.69 | 0.82 | 58 | empty |
| 2 | 315 | 0.64 | 0.80 | 45 | empty |
| 3 | 174 | 0.53 | 0.79 | 28 | empty |
| 4 | 60 | 0.28 | 0.73 | 14 | empty |
| 5 | 59 | 0.27 | 0.73 | 13 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1678 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1642 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 562 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 555 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7X9E · Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide · 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 P0DTC2
- Elsewhere: RCSB PDB 7X9E · PDBe 7X9E · UniProt P0DTC2
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