Research workbench
2.9 ångströms resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten
Analyse 2.9 ångströms resolution structure of an anti-dinitrophenyl-spin-label… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BAF
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa AN02 Fab (light chain); IGG1-kappa AN02 Fab (heavy chain)
- Ligands
- NPP
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa AN02 Fab (light chain) | protein | 214 | 6% helix, 55% strand | — |
| H | IGG1-kappa AN02 Fab (heavy chain) | protein | 217 | 3% helix, 50% strand | — |
Ligands and binding sites
- NPP · N-(2-amino-ethyl)-4,6-dinitro-N'-(2,2,6,6-tetramethyl-1-oxy-piperidin-4-yl)-benzene-1,3-diamine · 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 | 310 | 0.54 | 0.75 | 40 | empty |
| 2 | 171 | 0.52 | 0.79 | 27 | empty |
| 3 | 62 | 0.38 | 0.79 | 15 | NPP |
| 4 | 76 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1952 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1BAF · 2.9 ångströms resolution structure of an anti-dinitrophenyl-spin-label monoclonal… · 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
- Elsewhere: RCSB PDB 1BAF · PDBe 1BAF
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