Research workbench
An autoantibody to single-stranded DNA: comparison of the three- dimensional structures of the unliganded Fab and a deoxynucleotide- Fab complex
Analyse An autoantibody to single-stranded DNA: comparison of the three- dimensional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CBV
- Type
- protein + DNA
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*TP*T)-3'); Protein (Fab (BV04-01) autoantibody-light chain); Protein (Fab…
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*TP*TP*T)-3') | dna | 3 | — | — |
| L | Protein (Fab (BV04-01) autoantibody-light chain) | protein | 219 | 5% helix, 47% strand | — |
| H | Protein (Fab (BV04-01) autoantibody-heavy chain) | protein | 219 | 4% helix, 50% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.55 | 0.89 | 15 | empty |
| 2 | 207 | 0.45 | 0.73 | 31 | empty |
| 3 | 151 | 0.44 | 0.76 | 27 | empty |
| 4 | 97 | 0.38 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1834 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 334 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–L · 252 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1CBV · An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of… · the same entry in another collection · chain D against D, 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 1CBV · PDBe 1CBV
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