Research workbench
Crystal structure of an antitoxin part of a putative TOXIN/ANTITOXIN system (SWOL_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a resolution
Analyse Crystal structure of an antitoxin part of a putative TOXIN/ANTITOXIN system… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K6Q
- Type
- protein
- Length
- 553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ligand binding protein
- UniProt
- Q0AZ30
- Ligands
- MG, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ligand binding protein | protein | 139 | 48% helix, 27% strand | Q0AZ30 |
| B, C, D | Putative ligand binding protein | protein | 138 | 48% helix, 28% strand | Q0AZ30 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.76 | 0.81 | 61 | EDO |
| 2 | 220 | 0.54 | 0.77 | 26 | empty |
| 3 | 232 | 0.48 | 0.74 | 36 | empty |
| 4 | 131 | 0.42 | 0.76 | 21 | empty |
| 5 | 72 | 0.36 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1949 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1930 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 61 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3K6Q · CRYSTAL STRUCTURE OF An antitoxin part of a putative toxin/antitoxin system (SWOL_0700)… · 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 Q0AZ30
- Elsewhere: RCSB PDB 3K6Q · PDBe 3K6Q · UniProt Q0AZ30
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