Research workbench
Fab structure of antibody S1-15 in complex with ssdna DNA, 5'-5(DT)-P- 3'
Analyse Fab structure of antibody S1-15 in complex with ssdna DNA, 5'-5(DT)-P- 3' in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z95
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S1-15 Fab (IGG2B) heavy chain; S1-15 Fab (IGG2B) light chain
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S1-15 Fab (IGG2B) heavy chain | protein | 226 | 12% helix, 50% strand | — |
| L | S1-15 Fab (IGG2B) light chain | protein | 214 | 8% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.62 | 0.74 | 65 | empty |
| 2 | 201 | 0.56 | 0.79 | 29 | empty |
| 3 | 73 | 0.34 | 0.75 | 19 | empty |
| 4 | 79 | 0.33 | 0.75 | 22 | empty |
| 5 | 83 | 0.32 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- H–L · 1974 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4Z95 · Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(dT)-p-3' · the same entry in another collection · chain H against H, 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 4Z95 · PDBe 4Z95
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