Research workbench
Crystal structure of pseudomonas aeruginosa ligd polymerase domain with ATP and manganese
Analyse Crystal structure of pseudomonas aeruginosa ligd polymerase domain with ATP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FAQ
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent DNA ligase
- UniProt
- Q9I1X7
- Ligands
- ATP, MN, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable ATP-dependent DNA ligase | protein | 295 | 31% helix, 20% strand | Q9I1X7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, 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 | 596 | 0.71 | 0.79 | 48 | SO4 |
| 2 | 158 | 0.53 | 0.80 | 26 | empty |
| 3 | 165 | 0.51 | 0.78 | 27 | empty |
| 4 | 108 | 0.37 | 0.75 | 21 | MN, ATP |
| 5 | 84 | 0.33 | 0.74 | 18 | MN, ATP |
Interfaces
1 interface between chains.
- A–B · 876 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2FAQ · Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I1X7 · AlphaFold monomer V2.0 prediction for multifunctional non-homologous end joining protein… · a predicted model of the same protein · 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 Q9I1X7
- Elsewhere: RCSB PDB 2FAQ · PDBe 2FAQ · UniProt Q9I1X7
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