Research workbench
Crystal structure of C. thermocellum pnkp ligase domain in complex with ATP
Analyse Crystal structure of C. thermocellum pnkp ligase domain in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY5
- Type
- protein
- Length
- 762 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
- Ligands
- ATP, ADP
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% 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 | 381 | 45% helix, 18% strand | A3DJ38 |
| B | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 381 | 43% helix, 17% strand | A3DJ38 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.84 | 0.85 | 101 | ATP |
| 2 | 1131 | 0.82 | 0.83 | 93 | ADP, PGE |
| 3 | 169 | 0.50 | 0.77 | 19 | empty |
| 4 | 93 | 0.47 | 0.81 | 20 | empty |
| 5 | 84 | 0.42 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2191 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3TY5 · Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP · 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 3TY5 · PDBe 3TY5 · UniProt A3DJ38
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