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
- 1MRC
- Type
- protein
- Length
- 420 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
- ZN, SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% 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 | 204 | 4% helix, 52% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains L
- SO4 · Sulfate ion · ion · chains L, H
- IMD · Imidazole · additive · chains L
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 | 403 | 0.58 | 0.75 | 44 | empty |
| 2 | 109 | 0.40 | 0.76 | 21 | empty |
| 3 | 92 | 0.33 | 0.73 | 24 | empty |
| 4 | 69 | 0.32 | 0.75 | 17 | empty |
| 5 | 65 | 0.28 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1621 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MRC · 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 1MRC · PDBe 1MRC
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