Research workbench
Crystal structure of C. thermocellum pnkp ligase domain apo form
Analyse Crystal structure of C. thermocellum pnkp ligase domain apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY8
- Type
- protein
- Length
- 758 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide…
- EC
- 6.5.1.3
- UniProt
- A3DJ38
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 379 | 48% helix, 17% strand | A3DJ38 |
| B | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 379 | 45% helix, 17% strand | A3DJ38 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.84 | 0.85 | 121 | TAR |
| 2 | 1160 | 0.83 | 0.84 | 95 | GOL |
| 3 | 76 | 0.48 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2051 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3TY8 · Crystal Structure of C. Thermocellum PNKP Ligase Domain Apo Form · 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 A3DJ38
- Elsewhere: RCSB PDB 3TY8 · PDBe 3TY8 · UniProt A3DJ38
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