Research workbench
Crystal structure of the E.COLI polyphosphate kinase in complex with amppnp
Analyse Crystal structure of the E.COLI polyphosphate kinase in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XDP
- Type
- protein
- Length
- 1,374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyphosphate kinase
- EC
- 2.7.4.1
- UniProt
- P0A7B1
- Ligands
- ATP, MG
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyphosphate kinase (EC 2.7.4.1) | protein | 687 | 37% helix, 22% strand | P0A7B1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.77 | 0.81 | 65 | MG, ATP |
| 2 | 560 | 0.76 | 0.83 | 59 | empty |
| 3 | 718 | 0.75 | 0.81 | 56 | MG, ATP |
| 4 | 584 | 0.75 | 0.82 | 58 | empty |
| 5 | 240 | 0.64 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1799 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1XDP · Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7B1 · AlphaFold monomer V2.0 prediction for polyphosphate kinase (P0A7B1) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0A7B1
- Elsewhere: RCSB PDB 1XDP · PDBe 1XDP · UniProt P0A7B1
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