Research workbench
Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 ångströms
Analyse Crystal structures of an antibody to a peptide and its complex with peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IGF
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa B13I2 Fab (light chain); IGG1-kappa B13I2 Fab (heavy chain); Peptide (residues…
- UniProt
- P02247
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa B13I2 Fab (light chain) | protein | 219 | 5% helix, 49% strand | — |
| H | IGG1-kappa B13I2 Fab (heavy chain) | protein | 221 | 5% helix, 49% strand | — |
| P | Peptide (residues 69-87 of myohemerythrin) | protein | 7 | 0% helix, 0% strand | P02247 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.43 | 0.74 | 34 | empty |
| 2 | 116 | 0.41 | 0.76 | 18 | empty |
| 3 | 98 | 0.39 | 0.76 | 17 | empty |
| 4 | 109 | 0.37 | 0.74 | 26 | empty |
| 5 | 77 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1922 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 504 Ų buried · 10 hydrogen bonds · protein-protein
- L–P · 178 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2IGF · Crystal structures of an antibody to a peptide and its complex with peptide antigen at… · the same entry in another collection · chain L against L, TM-score 1.00
- P02247 · AlphaFold monomer V2.0 prediction for myohemerythrin (P02247) · a predicted model of the same protein · chain P against A, TM-score 0.43
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 P02247
- Elsewhere: RCSB PDB 2IGF · PDBe 2IGF · UniProt P02247
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