Research workbench
Orthorhombic form of IGG1 Fab fragment (in complex with antigenic tubulin peptide) sharing same fv as IgA
Analyse Orthorhombic form of IGG1 Fab fragment (in complex with antigenic tubulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QNZ
- Type
- protein
- Length
- 430 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
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab fragment of immunoglobulin G1 light chain | protein | 219 | 6% helix, 50% strand | — |
| B | Fab fragment of immunoglobulin G1 heavy chain | protein | 208 | 10% helix, 51% strand | — |
| C | Peptide from tubulin beta chain | protein | 3 | 0% helix, 0% strand | P07437 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.65 | 0.75 | 71 | empty |
| 2 | 155 | 0.43 | 0.74 | 23 | empty |
| 3 | 81 | 0.33 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1508 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 160 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3QNZ · Orthorhombic form of IgG1 Fab fragment (in complex with antigenic tubulin peptide)… · the same entry in another collection · chain A against A, TM-score 1.00
- P07437 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P07437) · a predicted model of the same protein · chain C 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 3QNZ · PDBe 3QNZ · UniProt P07437
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