MolNFT v2 · #15680 · protein
Crystal Structure of HyHEL-63 complexed with HEL mutant K97A
1NBZ · antibody kappa light chain: “Crystal Structure of HyHEL-63 complexed with HEL mutant K97A”. X-ray diffraction at 1.85, 6 pockets (best druggability 0.68). MolNFT v2 #15680 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NBZ
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Gallus gallus; Mus musculus
- Molecule
- antibody kappa light chain; immunoglobulin gamma 1 chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P01865, P00698
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | antibody kappa light chain | protein | 214 | 6% helix, 52% strand | — |
| B | immunoglobulin gamma 1 chain | protein | 210 | 7% helix, 50% strand | P01865 |
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.68 | 0.86 | 31 | empty |
| 2 | 165 | 0.48 | 0.76 | 19 | empty |
| 3 | 80 | 0.38 | 0.76 | 14 | empty |
| 4 | 119 | 0.37 | 0.73 | 22 | empty |
| 5 | 84 | 0.31 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1893 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 583 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1NBZ · Crystal structure of hyhel-63 complexed with hel mutant K97A · the same entry in another collection · chain A against A, TM-score 1.00
- 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 P01865
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1NBZ · PDBe 1NBZ · UniProt P01865 · UniProt P00698
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