Research workbench
F124 Fab fragment from a monoclonal anti-PRES2 antibody
Analyse F124 Fab fragment from a monoclonal anti-PRES2 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F11
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F124 immunoglobulin (kappa light chain); F124 immunoglobulin (IGG1 heavy chain)
- UniProt
- P01665, P01837, Q65ZR6, P01869
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | F124 immunoglobulin (kappa light chain) | protein | 216 | 6% helix, 52% strand | P01665, P01837 |
| B, D | F124 immunoglobulin (IGG1 heavy chain) | protein | 218 | 9% helix, 50% strand | Q65ZR6, P01869 |
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 | 598 | 0.70 | 0.78 | 40 | empty |
| 2 | 471 | 0.60 | 0.75 | 45 | empty |
| 3 | 451 | 0.59 | 0.74 | 45 | empty |
| 4 | 90 | 0.46 | 0.81 | 23 | empty |
| 5 | 123 | 0.38 | 0.74 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1701 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1654 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 145 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1F11 · F124 Fab fragment from a monoclonal anti-PRES2 antibody · the same entry in another collection · chain A against A, TM-score 1.00
- P01869 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region, membrane-bound form… · a predicted model of the same protein · chain B against A, TM-score 0.53
- P01665 · AlphaFold monomer V2.0 prediction for ig kappa chain V-III region pc 7043 (P01665) · a predicted model of the same protein · chain A against A, TM-score 0.51
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain A against A, TM-score 0.47
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 P01665
- Every structure of UniProt P01837
- Every structure of UniProt Q65ZR6
- Every structure of UniProt P01869
- Elsewhere: RCSB PDB 1F11 · PDBe 1F11 · UniProt P01665 · UniProt P01837 · UniProt Q65ZR6 · UniProt P01869
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