MolNFT v1 · #318 · protein
Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody D1.3
1A2Y · IGG1-kappa D1.3 fv (light chain): “Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody D1.3”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.70). MolNFT v1 #318 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.