MolNFT v1 · #27336 · protein
Structure for antibody hyhel-63 Y33A mutant complexed with hen egg lysozyme
1XGP · Antibody kappa light chain: “Structure for antibody hyhel-63 Y33A mutant complexed with hen egg lysozyme”. X-ray diffraction, 7 pockets (best druggability 0.67). MolNFT v1 #27336 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1XGP
- Type
- protein
- Length
- 554 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody kappa light chain; Antibody kappa heavy chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody kappa light chain | protein | 215 | 6% helix, 52% strand | — |
| B | Antibody kappa heavy chain | protein | 210 | 7% helix, 52% strand | — |
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.67 | 0.84 | 40 | empty |
| 2 | 279 | 0.49 | 0.73 | 41 | empty |
| 3 | 158 | 0.47 | 0.76 | 23 | empty |
| 4 | 112 | 0.39 | 0.75 | 18 | empty |
| 5 | 73 | 0.33 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1865 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 502 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1XGP · Structure for antibody HyHEL-63 Y33A mutant complexed with hen egg lysozyme · the same entry in another collection · chain A against A, 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
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1XGP · PDBe 1XGP · UniProt P00698
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