Research workbench
Crystal structure of hyhel-63 complexed with hel mutant K96A
Analyse Crystal structure of hyhel-63 complexed with hel mutant K96A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NBY
- 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 0.65
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, 50% strand | P01837 |
| B | Immunoglobulin gamma 1 chain | protein | 210 | 7% helix, 52% strand | P01865 |
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
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 | 224 | 0.65 | 0.83 | 35 | empty |
| 2 | 324 | 0.55 | 0.75 | 44 | empty |
| 3 | 154 | 0.47 | 0.76 | 20 | empty |
| 4 | 92 | 0.38 | 0.76 | 17 | empty |
| 5 | 53 | 0.26 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1802 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 597 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1NBY · Crystal Structure of HyHEL-63 complexed with HEL mutant K96A · 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 0.48
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 1NBY · PDBe 1NBY · UniProt P01837 · UniProt P01865 · UniProt P00698
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