Research workbench
Methylmercury chloride derivative structure of the lytic chapk domain of the endolysin lysk from staphylococcus aureus bacteriophage K
Analyse Methylmercury chloride derivative structure of the lytic chapk domain of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CT3
- Type
- protein
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF30/ORF32
- UniProt
- Q6Y7T6
- Ligands
- MMC, CMH, HG, CA, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ORF30/ORF32 | protein | 163 | 20% helix, 24% strand | Q6Y7T6 |
Ligands and binding sites
- MMC · Methyl mercury ion · ligand · 8 copies · chains A, B, C, D
- CMH · S-(methylmercury)-L-cysteine · ligand · 4 copies · chains A, B, C, D
- HG · Mercury (II) ion · metal · 6 copies · chains A, C, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.76 | 0.79 | 83 | CMH, CL, EPE, HG, GOL |
| 2 | 177 | 0.48 | 0.76 | 25 | CMH, CL, EPE |
| 3 | 149 | 0.47 | 0.77 | 26 | CMH, EPE, HG |
| 4 | 113 | 0.41 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 167 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
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 Q6Y7T6
- Elsewhere: RCSB PDB 4CT3 · PDBe 4CT3 · UniProt Q6Y7T6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.