Research workbench
Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody D1.3
Analyse Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A2Y
- Type
- protein
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa D1.3 fv (light chain); IGG1-kappa D1.3 fv (heavy chain); Lysozyme
- EC
- 3.2.1.17
- UniProt
- P01635, P01820, P00698
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG1-kappa D1.3 fv (light chain) | protein | 107 | 3% helix, 50% strand | P01635 |
| B | IGG1-kappa D1.3 fv (heavy chain) | protein | 116 | 8% helix, 52% strand | P01820 |
| C | Lysozyme (EC 3.2.1.17) | protein | 129 | 39% helix, 11% strand | P00698 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, C
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 | 108 | 0.70 | 0.92 | 24 | empty |
| 2 | 62 | 0.45 | 0.83 | 14 | PO4 |
| 3 | 55 | 0.30 | 0.75 | 12 | empty |
| 4 | 71 | 0.30 | 0.74 | 15 | empty |
| 5 | 74 | 0.28 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 841 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1A2Y · Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody D1.3 · the same entry in another collection · chain A against A, TM-score 1.00
- P01635 · AlphaFold monomer V2.0 prediction for ig kappa chain V-V region K2 (P01635) · a predicted model of the same protein · chain A against A, TM-score 0.87
- P01820 · AlphaFold monomer V2.0 prediction for ig heavy chain V region PJ14 (P01820) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 P01635
- Every structure of UniProt P01820
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1A2Y · PDBe 1A2Y · UniProt P01635 · UniProt P01820 · UniProt P00698
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