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Crystal structure of C. thermocellum pnkp ligase domain AMP-adenylate
Analyse Crystal structure of C. thermocellum pnkp ligase domain AMP-adenylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY9
- Type
- protein
- Length
- 1,500 residues
- Chains
- 4
- 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
- AMP, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% 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 | 376 | 50% helix, 17% strand | A3DJ38 |
| B | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 374 | 48% helix, 17% strand | A3DJ38 |
| C | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 376 | 50% helix, 17% strand | A3DJ38 |
| D | Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase (EC 6.5.1.3) | protein | 374 | 50% helix, 17% strand | A3DJ38 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, D, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.83 | 0.88 | 84 | AMP, MPD |
| 2 | 592 | 0.83 | 0.88 | 84 | AMP, MPD, GOL |
| 3 | 833 | 0.78 | 0.81 | 91 | empty |
| 4 | 443 | 0.77 | 0.86 | 55 | AMP, MPD |
| 5 | 391 | 0.77 | 0.86 | 55 | AMP |
Interfaces
6 interfaces between chains.
- C–D · 761 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 682 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 147 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3TY9 · Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate · 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 3TY9 · PDBe 3TY9 · UniProt A3DJ38
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