MolNFT v1 · #76541 · protein
Monoclinic form of IGG1 Fab fragment (in complex with antigenic peptide) sharing same fv as IgA
3QO0 · Fab fragment of immunoglobulin G1 light chain: “Monoclinic form of IGG1 Fab fragment (in complex with antigenic peptide) sharing same fv as IgA”. X-ray diffraction, 5 pockets (best druggability 0.64). MolNFT v1 #76541 on GenesisL1…
- 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
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