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Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide
Analyse Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CXD
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of anti-osteopontin antibody 23C3, light chain; Fab fragment of…
- UniProt
- P10451
- Ligands
- NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab fragment of anti-osteopontin antibody 23C3, light chain | protein | 213 | 3% helix, 51% strand | — |
| H | Fab fragment of anti-osteopontin antibody 23C3, heavy chain | protein | 216 | 7% helix, 49% strand | — |
| P | A peptide from osteopontin | protein | 9 | 0% helix, 0% strand | P10451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.54 | 0.81 | 21 | empty |
| 2 | 302 | 0.53 | 0.74 | 30 | empty |
| 3 | 66 | 0.49 | 0.85 | 21 | empty |
| 4 | 123 | 0.37 | 0.73 | 22 | empty |
| 5 | 50 | 0.36 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1671 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 417 Ų buried · 12 hydrogen bonds · protein-protein
- L–P · 278 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3CXD · Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide · the same entry in another collection · chain L against L, TM-score 1.00
- P10451 · AlphaFold monomer V2.0 prediction for osteopontin (P10451) · a predicted model of the same protein · chain P against A, TM-score 0.44
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P10451
- Elsewhere: RCSB PDB 3CXD · PDBe 3CXD · UniProt P10451
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