Research workbench
Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning
Analyse Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XF4
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| H, B | Fab heavy chain | protein | 213 | 8% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.60 | 0.75 | 67 | empty |
| 2 | 460 | 0.59 | 0.74 | 56 | empty |
| 3 | 89 | 0.32 | 0.73 | 25 | empty |
| 4 | 62 | 0.31 | 0.75 | 19 | empty |
| 5 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1688 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1663 Ų buried · 17 hydrogen bonds · protein-protein
- H–B · 157 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1XF4 · Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect… · 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 1XF4 · PDBe 1XF4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.