Research workbench
MERS S ectodomain trimer in complex with neutralizing antibody 6516
Analyse MERS S ectodomain trimer in complex with neutralizing antibody 6516 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V3L
- Type
- protein
- Length
- 4,710 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody H; Antibody L
- UniProt
- K0BRG7
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 18% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1131 | 21% helix, 22% strand | K0BRG7 |
| B | Spike glycoprotein | protein | 1135 | 21% helix, 23% strand | K0BRG7 |
| C | Spike glycoprotein | protein | 1126 | 21% helix, 22% strand | K0BRG7 |
| D, F, H | Antibody H | protein | 226 | 5% helix, 43% strand | — |
| E, G | Antibody L | protein | 214 | 3% helix, 41% strand | — |
| I | Antibody L | protein | 212 | 3% helix, 41% 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 | 834 | 0.82 | 0.85 | 105 | empty |
| 2 | 599 | 0.82 | 0.87 | 89 | empty |
| 3 | 637 | 0.82 | 0.87 | 85 | empty |
| 4 | 856 | 0.82 | 0.84 | 83 | empty |
| 5 | 714 | 0.81 | 0.85 | 78 | empty |
Interfaces
12 interfaces between chains.
- A–B · 3902 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3853 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 3697 Ų buried · 45 hydrogen bonds · protein-protein
- F–G · 2001 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1992 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 7V3L · MERS S ectodomain trimer in complex with neutralizing antibody 6516 · 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 7V3L · PDBe 7V3L · UniProt K0BRG7
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