Research workbench
Crystal structure of T6 Fab bound to thesars-cov-2 rbd of B.1.351
Analyse Crystal structure of T6 Fab bound to thesars-cov-2 rbd of B.1.351 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FJS
- Type
- protein
- Length
- 1,245 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T6 light chain; Spike protein S1; T6 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | T6 light chain | protein | 219 | 6% helix, 51% strand | — |
| E | Spike protein S1 | protein | 192 | 15% helix, 29% strand | P0DTC2 |
| H | T6 heavy chain | protein | 216 | 6% helix, 53% strand | — |
| B | Spike protein S1 | protein | 184 | 14% helix, 29% strand | P0DTC2 |
| C | T6 heavy chain | protein | 215 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1186 | 0.80 | 0.82 | 117 | empty |
| 2 | 523 | 0.60 | 0.74 | 63 | empty |
| 3 | 222 | 0.56 | 0.78 | 32 | empty |
| 4 | 50 | 0.54 | 0.90 | 20 | empty |
| 5 | 166 | 0.48 | 0.77 | 30 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1824 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1778 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 435 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 413 Ų buried · 4 hydrogen bonds · protein-protein
- L–B · 401 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7FJS · Crystal structure of T6 Fab bound to theSARS-CoV-2 RBD of B.1.351 · the same entry in another collection · chain L against L, 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 7FJS · PDBe 7FJS · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.