MolNFT v1 · #174919 · protein
Structure of sybody MR17-K99Y in complex with the SARS-cov-2 S receptor-binding domain (rbd)
7CAN: “Structure of sybody MR17-K99Y in complex with the SARS-cov-2 S receptor-binding domain (rbd)”. X-ray diffraction, 2 ligands (NAG, FUC). MolNFT v1 #174919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CAN
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sybody MR17-K99Y; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sybody MR17-K99Y | protein | 117 | 3% helix, 50% strand | — |
| B | Spike protein S1 | protein | 195 | 18% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 946 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7CAN · Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain… · 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 7CAN · PDBe 7CAN · UniProt P0DTC2
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