MolNFT v1 · #28852 · protein
The crystal structure of the antibody Fab HYHEL5 complex with lysozyme at 1.7A resolution
1YQV · Hyhel-5 antibody light chain: “The crystal structure of the antibody Fab HYHEL5 complex with lysozyme at 1.7A resolution”. X-ray diffraction, 6 pockets (best druggability 0.54). MolNFT v1 #28852 on GenesisL1: 3D structure, binding…
- 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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