Research workbench
Crystal structure of pseudomonas aeruginosa ligd polymerase domain with datp and manganese
Analyse Crystal structure of pseudomonas aeruginosa ligd polymerase domain with datp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FAR
- 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
- DTP, MN, SO4
- Pockets
- 5 · best druggability 0.69
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
- DTP · 2'-deoxyadenosine 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.69 | 0.79 | 50 | SO4 |
| 2 | 163 | 0.53 | 0.79 | 24 | empty |
| 3 | 166 | 0.50 | 0.78 | 28 | empty |
| 4 | 91 | 0.35 | 0.75 | 22 | MN, DTP |
| 5 | 76 | 0.32 | 0.75 | 20 | MN, DTP |
Interfaces
1 interface between chains.
- A–B · 874 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2FAR · Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP 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 2FAR · PDBe 2FAR · UniProt Q9I1X7
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