Research workbench
Crystal structure of a recombinant anti-single-stranded DNA antibody fragment complexed with DT5
Analyse Crystal structure of a recombinant anti-single-stranded DNA antibody fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I8M
- Type
- protein + DNA
- Length
- 858 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*TP*TP*T)-3'; 5'-D(P*TP*T)-3'; Antibody light chain Fab; Antibody heavy chain…
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*TP*TP*TP*TP*T)-3' | dna | 5 | — | — |
| D | 5'-D(P*TP*T)-3' | dna | 1 | — | — |
| L, A | Antibody light chain Fab | protein | 213 | 5% helix, 52% strand | — |
| H, B | Antibody heavy chain Fab | protein | 213 | 8% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.58 | 0.74 | 57 | empty |
| 2 | 331 | 0.57 | 0.76 | 44 | empty |
| 3 | 303 | 0.53 | 0.74 | 33 | empty |
| 4 | 66 | 0.31 | 0.74 | 15 | empty |
| 5 | 69 | 0.28 | 0.72 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1805 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1653 Ų buried · 18 hydrogen bonds · protein-protein
- T–H · 285 Ų buried · 4 hydrogen bonds · protein-nucleic
- T–L · 242 Ų buried · 4 hydrogen bonds · protein-nucleic
- T–B · 221 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1I8M · Crystal structure of a recombinant anti-single-stranded DNA antibody fragment complexed… · the same entry in another collection · chain T against T, 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 1I8M · PDBe 1I8M
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