Research workbench
Crystal structure of the anti-hinge rabbit antibody 2095-2 in complex with ides hinge peptide
Analyse Crystal structure of the anti-hinge rabbit antibody 2095-2 in complex with ides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O4Y
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2095-2 light chain; 2095-2 heavy chain; Ides hinge peptide
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 2095-2 light chain | protein | 219 | 8% helix, 51% strand | — |
| H | 2095-2 heavy chain | protein | 215 | 8% helix, 51% strand | — |
| A | Ides hinge peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains L, H
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 | 242 | 0.55 | 0.77 | 37 | empty |
| 2 | 332 | 0.53 | 0.74 | 50 | GOL |
| 3 | 105 | 0.36 | 0.74 | 19 | GOL |
| 4 | 61 | 0.32 | 0.76 | 16 | empty |
| 5 | 58 | 0.25 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1870 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 316 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 299 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 4O4Y · Crystal structure of the anti-hinge rabbit antibody 2095-2 in complex with IDES hinge… · 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 4O4Y · PDBe 4O4Y
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