Research workbench
SARS-cov-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two receptor-binding domains open)
Analyse SARS-cov-2 spike in complex with the S2K146 neutralizing antibody Fab fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TAT
- Type
- protein
- Length
- 3,564 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2K146 Fab heavy chain; S2K146 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 980 | 22% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 956 | 22% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 946 | 22% helix, 34% strand | P0DTC2 |
| H, D, F | S2K146 Fab heavy chain | protein | 120 | 3% helix, 49% strand | — |
| L, G | S2K146 Fab light chain | protein | 108 | 7% helix, 45% strand | — |
| E | S2K146 Fab light chain | protein | 106 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.87 | 0.88 | 104 | empty |
| 2 | 1174 | 0.85 | 0.86 | 151 | empty |
| 3 | 998 | 0.84 | 0.85 | 120 | empty |
| 4 | 943 | 0.81 | 0.83 | 118 | empty |
| 5 | 1059 | 0.81 | 0.83 | 133 | empty |
Interfaces
12 interfaces between chains.
- A–C · 3682 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3611 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3155 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 469 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 363 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TAT · SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two… · 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 7TAT · PDBe 7TAT · UniProt P0DTC2
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