Research workbench
SARS-cov-2 receptor binding domain in complex with AB17
Analyse SARS-cov-2 receptor binding domain in complex with AB17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TE1
- Type
- protein
- Length
- 1,178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AB17 heavy chain; AB17 light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | AB17 heavy chain | protein | 209 | 1% helix, 50% strand | — |
| F | AB17 light chain | protein | 210 | 6% helix, 46% strand | — |
| H | AB17 heavy chain | protein | 206 | 1% helix, 45% strand | — |
| L | AB17 light chain | protein | 196 | 5% helix, 46% strand | — |
| D | Spike protein S1 | protein | 170 | 18% helix, 25% strand | P0DTC2 |
| E | Spike protein S1 | protein | 187 | 16% helix, 28% strand | P0DTC2 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.74 | 0.77 | 107 | empty |
| 2 | 662 | 0.68 | 0.77 | 66 | empty |
| 3 | 68 | 0.58 | 0.89 | 24 | empty |
| 4 | 106 | 0.49 | 0.81 | 20 | empty |
| 5 | 115 | 0.44 | 0.78 | 18 | empty |
Interfaces
10 interfaces between chains.
- C–F · 1949 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- H–D · 680 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 597 Ų buried · 4 hydrogen bonds · protein-protein
- L–D · 539 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 7TE1 · SARS-CoV-2 Receptor Binding Domain in Complex with Ab17 · the same entry in another collection · chain H against H, 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 7TE1 · PDBe 7TE1 · UniProt P0DTC2
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