Research workbench
Crystal structure of Fab fragment of antibody hyhel-8 complexed with its antigen lysozyme
Analyse Crystal structure of Fab fragment of antibody hyhel-8 complexed with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NDG
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody kappa light chain; Immunoglobulin gamma 1 chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P01837, P01865, P00698
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody kappa light chain | protein | 214 | 6% helix, 51% strand | P01837 |
| B | Immunoglobulin gamma 1 chain | protein | 210 | 7% helix, 51% strand | P01865 |
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Ligands and binding sites
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.68 | 0.88 | 29 | ACY |
| 2 | 477 | 0.59 | 0.74 | 50 | empty |
| 3 | 172 | 0.48 | 0.76 | 20 | empty |
| 4 | 77 | 0.33 | 0.75 | 17 | empty |
| 5 | 51 | 0.26 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1838 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 611 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1NDG · Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme · the same entry in another collection · chain A against A, TM-score 1.00
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain A against A, TM-score 0.49
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain B against A, TM-score 0.49
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 P01837
- Every structure of UniProt P01865
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1NDG · PDBe 1NDG · UniProt P01837 · UniProt P01865 · UniProt P00698
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