Research workbench
Crystal structure of MERS-cov neutralizing antibody G4 Fab
Analyse Crystal structure of MERS-cov neutralizing antibody G4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VZR
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G4 antibody heavy chain; G4 antibody light chain
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | G4 antibody heavy chain | protein | 218 | 10% helix, 54% strand | — |
| L | G4 antibody light chain | protein | 209 | 6% helix, 55% strand | — |
| A | G4 antibody heavy chain | protein | 217 | 10% helix, 54% strand | — |
| B | G4 antibody light chain | protein | 208 | 6% helix, 54% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.59 | 0.80 | 31 | empty |
| 2 | 366 | 0.54 | 0.74 | 47 | empty |
| 3 | 84 | 0.52 | 0.85 | 24 | empty |
| 4 | 78 | 0.48 | 0.83 | 23 | empty |
| 5 | 233 | 0.47 | 0.73 | 30 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1896 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1820 Ų buried · 17 hydrogen bonds · protein-protein
- H–B · 290 Ų buried · 2 hydrogen bonds · protein-protein
- H–A · 107 Ų buried · 0 hydrogen bonds · protein-protein
- L–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5VZR · Crystal Structure of MERS-CoV neutralizing antibody G4 Fab · the same entry in another collection · chain H against H, 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 5VZR · PDBe 5VZR
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