Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody K288.2
Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TP3
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; K288.2 heavy chain; K288.2 light chain
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Spike protein S1 | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| H | K288.2 heavy chain | protein | 231 | 9% helix, 52% strand | — |
| L | K288.2 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 3 copies · chains Z, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.54 | 0.74 | 41 | CAC |
| 2 | 137 | 0.43 | 0.76 | 18 | empty |
| 3 | 113 | 0.40 | 0.75 | 22 | empty |
| 4 | 99 | 0.37 | 0.75 | 23 | CAC |
| 5 | 66 | 0.35 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2020 Ų buried · 14 hydrogen bonds · protein-protein
- Z–H · 591 Ų buried · 11 hydrogen bonds · protein-protein
- Z–L · 264 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7TP3 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · the same entry in another collection · chain Z against Z, 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 7TP3 · PDBe 7TP3 · UniProt P0DTC2
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