Research workbench
Catalytic antibody D2.3 complex
Analyse Catalytic antibody D2.3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YEI
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ig antibody D2.3 (light chain)); Protein (ig antibody D2.3 (heavy chain))
- Ligands
- PGG, ZN
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (ig antibody D2.3 (light chain)) | protein | 219 | 5% helix, 52% strand | — |
| H | Protein (ig antibody D2.3 (heavy chain)) | protein | 222 | 7% helix, 53% strand | — |
Ligands and binding sites
- PGG · Para-nitrophenylphosphonobutanoyl-glycine · ligand · chains L, H
- ZN · Zinc ion · metal · 7 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.62 | 0.85 | 28 | PGG |
| 2 | 162 | 0.40 | 0.73 | 29 | empty |
| 3 | 54 | 0.34 | 0.78 | 12 | empty |
| 4 | 59 | 0.27 | 0.73 | 19 | empty |
| 5 | 50 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 2108 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1YEI · Catalytic antibody D2.3 complex · 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 1YEI · PDBe 1YEI
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