Research workbench
Cationic cyclization antibody 4C6 complex with transition state analog
Analyse Cationic cyclization antibody 4C6 complex with transition state analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ND0
- Type
- protein
- Length
- 1,764 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin IGG2A
- UniProt
- Q8K0F8, P01865
- Ligands
- DP4, SO4
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Immunoglobulin IGG2A | protein | 219 | 6% helix, 54% strand | Q8K0F8 |
| B, D, F, H | Immunoglobulin IGG2A | protein | 222 | 5% helix, 51% strand | P01865 |
Ligands and binding sites
- DP4 · (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.69 | 0.89 | 16 | DP4 |
| 2 | 139 | 0.68 | 0.89 | 17 | DP4 |
| 3 | 137 | 0.68 | 0.89 | 17 | DP4 |
| 4 | 467 | 0.68 | 0.79 | 50 | empty |
| 5 | 141 | 0.67 | 0.88 | 18 | DP4 |
Interfaces
7 interfaces between chains.
- G–H · 2108 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2079 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2076 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2068 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 1ND0 · Cationic cyclization antibody 4C6 complex with transition state analog · the same entry in another collection · chain G against G, 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 0.52
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 Q8K0F8
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1ND0 · PDBe 1ND0 · UniProt Q8K0F8 · UniProt P01865
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