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The crystal structure of the antibody Fab HYHEL5 complex with lysozyme at 1.7A resolution
Analyse The crystal structure of the antibody Fab HYHEL5 complex with lysozyme at 1.7A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YQV
- Type
- protein
- Length
- 555 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyhel-5 antibody light chain; Hyhel-5 antibody heavy chain; Hen egg white lysozyme
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Hyhel-5 antibody light chain | protein | 211 | 6% helix, 51% strand | — |
| H | Hyhel-5 antibody heavy chain | protein | 215 | 8% helix, 52% strand | — |
| Y | Hen egg white lysozyme (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.54 | 0.79 | 35 | empty |
| 2 | 86 | 0.53 | 0.85 | 24 | empty |
| 3 | 322 | 0.52 | 0.74 | 39 | empty |
| 4 | 104 | 0.39 | 0.76 | 21 | empty |
| 5 | 71 | 0.33 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1768 Ų buried · 23 hydrogen bonds · protein-protein
- H–Y · 516 Ų buried · 13 hydrogen bonds · protein-protein
- L–Y · 405 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1YQV · The crystal structure of the antibody Fab HyHEL5 complex with lysozyme at 1.7A resolution · 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
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1YQV · PDBe 1YQV · UniProt P00698
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