Research workbench
Evidence for the extended helical nature of polysaccharide epitopes. the 2.8 ångströms resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2->8)- polysialic acid
Analyse Evidence for the extended helical nature of polysaccharide epitopes. the 2.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PLG
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A=KAPPA=
- UniProt
- P01865
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A=KAPPA= | protein | 215 | 6% helix, 54% strand | — |
| H | IGG2A=KAPPA= | protein | 215 | 4% helix, 52% strand | P01865 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.56 | 0.76 | 32 | empty |
| 2 | 70 | 0.31 | 0.74 | 19 | empty |
| 3 | 83 | 0.31 | 0.73 | 12 | empty |
| 4 | 62 | 0.29 | 0.74 | 20 | empty |
| 5 | 61 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1794 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1PLG · Evidence for the extended helical nature of polysaccharide epitopes. the 2.8 ångströms… · the same entry in another collection · chain L against L, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.48
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 P01865
- Elsewhere: RCSB PDB 1PLG · PDBe 1PLG · UniProt P01865
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