Research workbench
Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5
Analyse Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SYC
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- LYE, NA, CL
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
| B | Lysozyme (EC 3.2.1.17) | protein | 128 | 45% helix, 11% strand | P00698 |
Ligands and binding sites
- LYE · bromophenol blue · ligand · 8 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.61 | 0.77 | 51 | IMD |
| 2 | 72 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 340 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6SYC · Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5 · the same entry in another collection · chain A against A, 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 6SYC · PDBe 6SYC · UniProt P00698
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.