MolNFT v1 · #164450 · protein
Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5
6SYC: “Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5”. X-ray diffraction, 3 ligands (LYE, NA, CL), 2 pockets (best druggability 0.61). MolNFT v1 #164450 on GenesisL1: 3D structure, binding sites and pockets in…
- 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
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