Research workbench
Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. crystal structures of native Fab and three Fab-mononucleotide complexes
Analyse Preparation, characterization and crystallization of an antibody Fab fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MRD
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2B-kappa JEL103 Fab (light chain); IGG2B-kappa JEL103 Fab (heavy chain)
- Ligands
- IDP, ZN
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2B-kappa JEL103 Fab (light chain) | protein | 216 | 6% helix, 52% strand | — |
| H | IGG2B-kappa JEL103 Fab (heavy chain) | protein | 208 | 7% helix, 55% strand | — |
Ligands and binding sites
- IDP · Inosine-5'-diphosphate · ligand · chains L, H
- ZN · Zinc ion · metal · chains L
- IMD · Imidazole · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.45 | 0.74 | 31 | empty |
| 2 | 111 | 0.43 | 0.77 | 22 | empty |
| 3 | 114 | 0.37 | 0.74 | 16 | empty |
| 4 | 61 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1686 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MRD · Preparation, characterization and crystallization of an antibody Fab fragment that… · 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 1MRD · PDBe 1MRD
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