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
- 5ZXV
- Type
- protein
- Length
- 1,254 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov rbd; Heavy chain; Light chain
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MERS-cov rbd | protein | 208 | 17% helix, 36% strand | — |
| H, C | Heavy chain | protein | 213 | 6% helix, 46% strand | — |
| L, D | Light chain | protein | 206 | 4% helix, 52% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.73 | 0.82 | 49 | empty |
| 2 | 54 | 0.72 | 0.98 | 19 | empty |
| 3 | 517 | 0.68 | 0.79 | 65 | empty |
| 4 | 429 | 0.56 | 0.73 | 51 | empty |
| 5 | 311 | 0.53 | 0.74 | 44 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1597 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1590 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 657 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 616 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 481 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5ZXV · 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 5ZXV · PDBe 5ZXV
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