Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing human antibody wrair-2151.
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
- 7N4M
- Type
- protein
- Length
- 537 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wrair-2151 antibody Fab heavy chain; Spike protein S1; Wrair-2151 antibody Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Wrair-2151 antibody Fab heavy chain | protein | 121 | 2% helix, 44% strand | — |
| A | Spike protein S1 | protein | 202 | 15% helix, 28% strand | P0DTC2 |
| L | Wrair-2151 antibody Fab light chain | protein | 214 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.54 | 0.77 | 46 | empty |
| 2 | 129 | 0.39 | 0.74 | 26 | empty |
| 3 | 70 | 0.29 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 884 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 415 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 376 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7N4M · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 7N4M · PDBe 7N4M · UniProt P0DTC2
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