MolNFT v1 · #27281 · protein + DNA
Structure of Fab DNA-1 complexed with DT3
1XF2 · 5'-D(*TP*TP*T)-3': “Structure of Fab DNA-1 complexed with DT3”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.62). MolNFT v1 #27281 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XF2
- Type
- protein + DNA
- Length
- 854 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*T)-3'; Antibody light chain Fab; Antibody heavy chain Fab
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*TP*TP*T)-3' | dna | 2 | — | — |
| L, A | Antibody light chain Fab | protein | 213 | 5% helix, 51% strand | — |
| H, B | Antibody heavy chain Fab | protein | 213 | 8% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, A
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 | 483 | 0.62 | 0.75 | 59 | empty |
| 2 | 237 | 0.49 | 0.75 | 34 | empty |
| 3 | 156 | 0.48 | 0.78 | 23 | empty |
| 4 | 63 | 0.28 | 0.73 | 17 | empty |
| 5 | 51 | 0.26 | 0.73 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1805 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1706 Ų buried · 16 hydrogen bonds · protein-protein
- T–L · 220 Ų buried · 4 hydrogen bonds · protein-nucleic
- T–H · 184 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1XF2 · Structure of Fab DNA-1 complexed with dT3 · 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 1XF2 · PDBe 1XF2
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