MolNFT v1 · #112851 · protein
Crystal structure of SGCC5 protein from streptomyces globisporus (complex with (R)-(-)-1-(2-naphthyl)-1,2-ethanediol and sucrose)
4ZXW · C-domain type II peptide synthetase: “Crystal structure of SGCC5 protein from streptomyces globisporus (complex with…”. X-ray diffraction, 4 ligands (4T7, GLC, FRU), 12 pockets (best druggability 0.86). MolNFT v1 #112851 on…
- PDB
- 4ZXW
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-domain type II peptide synthetase
- UniProt
- Q8GMG2
- Ligands
- 4T7, GLC, FRU, SO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-domain type II peptide synthetase | protein | 443 | 40% helix, 23% strand | Q8GMG2 |
Ligands and binding sites
- 4T7 · (1R)-1-(naphthalen-2-yl)ethane-1,2-diol · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.86 | 0.94 | 52 | GLC, FRU, 4T7 |
| 2 | 408 | 0.86 | 0.94 | 53 | GLC, FRU, 4T7 |
| 3 | 658 | 0.70 | 0.78 | 67 | empty |
| 4 | 175 | 0.63 | 0.84 | 29 | empty |
| 5 | 174 | 0.62 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4ZXW · Crystal structure of SgcC5 protein from Streptomyces globisporus (complex with… · 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 Q8GMG2
- Elsewhere: RCSB PDB 4ZXW · PDBe 4ZXW · UniProt Q8GMG2
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