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
- 1MRF
- Type
- protein
- Length
- 421 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
- DI, ZN
- Pockets
- 3 · best druggability 0.56
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, 53% strand | — |
| H | IGG2B-kappa JEL103 Fab (heavy chain) | protein | 205 | 9% helix, 55% strand | — |
Ligands and binding sites
- DI · 2'-deoxyinosine-5'-monophosphate · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.56 | 0.75 | 52 | empty |
| 2 | 100 | 0.39 | 0.76 | 18 | DI |
| 3 | 98 | 0.33 | 0.72 | 23 | empty |
Interfaces
1 interface between chains.
- L–H · 1649 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MRF · 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 1MRF · PDBe 1MRF
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.