Research workbench
Crystal structure of hyhel-10 fv MUTANT(HD32A)-hen lysozyme complex
Analyse Crystal structure of hyhel-10 fv MUTANT(HD32A)-hen lysozyme complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IC4
- 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; IGG1 Fab chain H; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P01642, P01823, P00698
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Lysozyme binding ig kappa chain | protein | 107 | 3% helix, 50% strand | P01642 |
| H | IGG1 Fab chain H | protein | 114 | 5% helix, 49% strand | P01823 |
| Y | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.66 | 0.86 | 28 | empty |
| 2 | 54 | 0.41 | 0.82 | 17 | empty |
| 3 | 80 | 0.36 | 0.75 | 15 | empty |
| 4 | 60 | 0.28 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 745 Ų buried · 5 hydrogen bonds · protein-protein
- H–Y · 555 Ų buried · 13 hydrogen bonds · protein-protein
- L–Y · 392 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1IC4 · Crystal structure of hyhel-10 fv MUTANT(HD32A)-hen lysozyme complex · the same entry in another collection · chain L against L, TM-score 1.00
- P01823 · AlphaFold monomer V2.0 prediction for ig heavy chain V region 36-60 (P01823) · a predicted model of the same protein · chain H against A, TM-score 0.95
- P01642 · AlphaFold monomer V2.0 prediction for ig kappa chain V-V region L7 (P01642) · a predicted model of the same protein · chain L against A, TM-score 0.87
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 P01642
- Every structure of UniProt P01823
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1IC4 · PDBe 1IC4 · UniProt P01642 · UniProt P01823 · UniProt P00698
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