Research workbench
Crystal structure of middle-east respiratory syndrome (MERS) coronavirus neutralizing antibody JC57-14 isolated from a vaccinated rhesus macaque in complex with MERS receptor binding domain
Analyse Crystal structure of middle-east respiratory syndrome (MERS) coronavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C6Y
- Type
- protein
- Length
- 1,268 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- JC57-14 heavy chain; JC57-14 light chain; Spike glycoprotein
- UniProt
- K9N5Q8
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | JC57-14 heavy chain | protein | 214 | 6% helix, 49% strand | — |
| B, L | JC57-14 light chain | protein | 214 | 5% helix, 50% strand | — |
| H | JC57-14 heavy chain | protein | 210 | 5% helix, 52% strand | — |
| R, S | Spike glycoprotein | protein | 208 | 10% helix, 33% strand | K9N5Q8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.71 | 0.89 | 26 | empty |
| 2 | 884 | 0.68 | 0.74 | 93 | empty |
| 3 | 403 | 0.65 | 0.79 | 47 | empty |
| 4 | 337 | 0.61 | 0.78 | 42 | empty |
| 5 | 275 | 0.54 | 0.76 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1710 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1692 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 756 Ų buried · 12 hydrogen bonds · protein-protein
- B–S · 610 Ų buried · 6 hydrogen bonds · protein-protein
- L–R · 575 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6C6Y · Crystal structure of Middle-East Respiratory Syndrome (MERS) coronavirus neutralizing… · 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 K9N5Q8
- Elsewhere: RCSB PDB 6C6Y · PDBe 6C6Y · UniProt K9N5Q8
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