Research workbench
Structure of Fab DNA-1 complexed with a stem-loop DNA ligand
Analyse Structure of Fab DNA-1 complexed with a stem-loop DNA ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FR4
- Type
- protein + DNA
- Length
- 873 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'; Antibody light chain Fab; Antibody heavy chain Fab
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N | 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3' | dna | 10 | — | — |
| L | Antibody light chain Fab | protein | 212 | 6% helix, 53% strand | — |
| H | Antibody heavy chain Fab | protein | 214 | 7% helix, 50% strand | — |
| A | Antibody light chain Fab | protein | 213 | 6% helix, 53% strand | — |
| B | Antibody heavy chain Fab | protein | 214 | 8% helix, 51% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 95 | empty |
| 2 | 435 | 0.58 | 0.74 | 49 | empty |
| 3 | 358 | 0.54 | 0.74 | 56 | empty |
| 4 | 195 | 0.53 | 0.78 | 38 | empty |
| 5 | 187 | 0.50 | 0.77 | 36 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1641 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1617 Ų buried · 15 hydrogen bonds · protein-protein
- M–B · 408 Ų buried · 7 hydrogen bonds · protein-nucleic
- M–N · 396 Ų buried · 17 hydrogen bonds · nucleic-nucleic
- N–H · 388 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2FR4 · Structure of Fab DNA-1 complexed with a stem-loop DNA ligand · the same entry in another collection · chain M against M, 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 2FR4 · PDBe 2FR4
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