Research workbench
Structural definition of a unique neutralization epitope on the receptor-binding domain of MERS-cov spike glycoprotein
Analyse Structural definition of a unique neutralization epitope on the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YY5
- Type
- protein
- Length
- 855 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov rbd; Heavy chain; Light chain
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MERS-cov rbd | protein | 209 | 17% helix, 34% strand | — |
| H | Heavy chain | protein | 111 | 5% helix, 50% strand | — |
| L | Light chain | protein | 112 | 0% helix, 45% strand | — |
| C | Heavy chain | protein | 109 | 3% helix, 45% strand | — |
| D | Light chain | protein | 105 | 0% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.61 | 0.75 | 73 | empty |
| 2 | 183 | 0.59 | 0.82 | 29 | empty |
| 3 | 287 | 0.50 | 0.73 | 30 | empty |
| 4 | 88 | 0.42 | 0.79 | 29 | empty |
| 5 | 134 | 0.42 | 0.75 | 24 | empty |
Interfaces
7 interfaces between chains.
- H–L · 792 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 748 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 673 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 619 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 450 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5YY5 · Structural definition of a unique neutralization epitope on the 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
- Elsewhere: RCSB PDB 5YY5 · PDBe 5YY5
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