Research workbench
MERS S ectodomain trimer in complex with neutralizing antibody 0722 (state 1)
Analyse MERS S ectodomain trimer in complex with neutralizing antibody 0722 (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V5K
- Type
- protein
- Length
- 4,725 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; Human betacoronavirus 2c EMC/2012
- Molecule
- Spike glycoprotein; 0722 L; 0722 H
- UniProt
- K0BRG7
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.8 · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1141 | 22% helix, 25% strand | K0BRG7 |
| D, F, H | 0722 L | protein | 212 | 5% helix, 49% strand | — |
| E, G, I | 0722 H | protein | 222 | 4% helix, 48% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.83 | 0.88 | 77 | empty |
| 2 | 1115 | 0.82 | 0.83 | 141 | empty |
| 3 | 685 | 0.82 | 0.86 | 69 | empty |
| 4 | 832 | 0.82 | 0.84 | 86 | empty |
| 5 | 790 | 0.80 | 0.83 | 72 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4874 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 4844 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 3805 Ų buried · 36 hydrogen bonds · protein-protein
- H–I · 1552 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1504 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide (disulfide).
Compared structures
- 7V5K · MERS S ectodomain trimer in complex with neutralizing antibody 0722 (state 1) · 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 K0BRG7
- Elsewhere: RCSB PDB 7V5K · PDBe 7V5K · UniProt K0BRG7
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