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Structure of an antibody-antigen complex. crystal structure of the HY/HEL-10 Fab-lysozyme complex
Analyse Structure of an antibody-antigen complex. crystal structure of the HY/HEL-10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HFM
- Type
- protein
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyhel-10 IGG1 Fab (light chain); Hyhel-10 IGG1 Fab (heavy chain); Hen egg white lysozyme
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Hyhel-10 IGG1 Fab (light chain) | protein | 214 | 6% helix, 44% strand | — |
| H | Hyhel-10 IGG1 Fab (heavy chain) | protein | 215 | 1% helix, 47% strand | — |
| Y | Hen egg white lysozyme (EC 3.2.1.17) | protein | 129 | 38% 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 | 638 | 0.64 | 0.74 | 54 | empty |
| 2 | 219 | 0.59 | 0.80 | 26 | empty |
| 3 | 202 | 0.59 | 0.81 | 24 | empty |
| 4 | 61 | 0.48 | 0.85 | 17 | empty |
| 5 | 83 | 0.40 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1933 Ų buried · 15 hydrogen bonds · protein-protein
- H–Y · 547 Ų buried · 13 hydrogen bonds · protein-protein
- L–Y · 383 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3HFM · Structure of an antibody-antigen complex. crystal structure of the HY/HEL-10 Fab-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 3HFM · PDBe 3HFM · UniProt P00698
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