Research workbench
Monoclinic form of IGG1 Fab fragment (in complex with antigenic peptide) sharing same fv as IgA
Analyse Monoclinic form of IGG1 Fab fragment (in complex with antigenic peptide)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QO0
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of immunoglobulin G1 light chain; Fab fragment of immunoglobulin G1 heavy…
- UniProt
- P07437
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab fragment of immunoglobulin G1 light chain | protein | 219 | 8% helix, 50% strand | — |
| B | Fab fragment of immunoglobulin G1 heavy chain | protein | 220 | 10% helix, 50% strand | — |
| C | Peptide from tubulin beta chain | protein | 2 | 0% helix, 0% strand | P07437 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.64 | 0.75 | 56 | empty |
| 2 | 134 | 0.44 | 0.76 | 22 | empty |
| 3 | 63 | 0.30 | 0.75 | 20 | empty |
| 4 | 57 | 0.28 | 0.74 | 17 | empty |
| 5 | 55 | 0.27 | 0.74 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1789 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 133 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3QO0 · Monoclinic form of IgG1 Fab fragment (in complex with antigenic peptide) sharing same Fv… · 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 P07437
- Elsewhere: RCSB PDB 3QO0 · PDBe 3QO0 · UniProt P07437
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.