Research workbench
48G7 hybridoma line Fab complexed with hapten 5-(para- nitrophenyl phosphonate)-pentanoic acid
Analyse 48G7 hybridoma line Fab complexed with hapten 5-(para- nitrophenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GAF
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric 48G7 Fab
- UniProt
- P01857
- Ligands
- NPE
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric 48G7 Fab | protein | 214 | 5% helix, 49% strand | — |
| H | Chimeric 48G7 Fab | protein | 217 | 11% helix, 49% strand | P01857 |
Ligands and binding sites
- NPE · 5-(para-nitrophenyl phosphonate)-pentanoic acid · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.69 | 0.92 | 20 | NPE |
| 2 | 515 | 0.60 | 0.74 | 59 | empty |
| 3 | 150 | 0.50 | 0.78 | 23 | empty |
| 4 | 88 | 0.33 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1817 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1GAF · 48G7 hybridoma line Fab complexed with hapten 5-(para-nitrophenyl phosphonate)-pentanoic… · the same entry in another collection · chain L against L, 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 P01857
- Elsewhere: RCSB PDB 1GAF · PDBe 1GAF · UniProt P01857
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