Research workbench
Crystal structure of the fv fragment of a monoclonal antibody specific for poly-glutamine
Analyse Crystal structure of the fv fragment of a monoclonal antibody specific for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GSG
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody light chain; Monoclonal antibody heavy chain
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Monoclonal antibody light chain | protein | 114 | 5% helix, 53% strand | — |
| B, D | Monoclonal antibody heavy chain | protein | 118 | 5% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.76 | 0.78 | 88 | empty |
| 2 | 166 | 0.48 | 0.77 | 30 | empty |
| 3 | 115 | 0.41 | 0.76 | 19 | empty |
| 4 | 72 | 0.31 | 0.74 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 926 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GSG · Crystal structure of the Fv fragment of a monoclonal antibody specific for poly-glutamine · 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 2GSG · PDBe 2GSG
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