Research workbench
Crystal structure of hyhel-10 fv mutant (HY53A) complexed with hen egg lysozyme
Analyse Crystal structure of hyhel-10 fv mutant (HY53A) complexed with hen egg lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQE
- Type
- protein
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme binding ig kappa chain V23-J2 region; Ig VH,ANTI-lysozyme; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Lysozyme binding ig kappa chain V23-J2 region | protein | 107 | 3% helix, 50% strand | — |
| H | Ig VH,ANTI-lysozyme | protein | 114 | 8% helix, 51% strand | — |
| Y | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.65 | 0.87 | 26 | empty |
| 2 | 90 | 0.35 | 0.75 | 24 | empty |
| 3 | 57 | 0.27 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 769 Ų buried · 5 hydrogen bonds · protein-protein
- H–Y · 545 Ų buried · 15 hydrogen bonds · protein-protein
- L–Y · 418 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2DQE · Crystal structure of hyhel-10 FV mutant (Hy53a) complexed with hen egg lysozyme · 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 2DQE · PDBe 2DQE · UniProt P00698
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