Research workbench
Crystal structure of polyphosphate kinase 2 class I (SMC02148) in complex with ADP
Analyse Crystal structure of polyphosphate kinase 2 class I (SMC02148) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZG
- Type
- protein
- Length
- 1,152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLYPHOSPHATE:ADP phosphotransferase 1
- EC
- 2.7.4.1
- UniProt
- Q92SA6
- Ligands
- MLT, ADP, AMP
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | POLYPHOSPHATE:ADP phosphotransferase 1 (EC 2.7.4.1) | protein | 288 | 47% helix, 15% strand | Q92SA6 |
Ligands and binding sites
- MLT · D-malate · ligand · 5 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.83 | 0.84 | 95 | ADP, MLT |
| 2 | 940 | 0.82 | 0.84 | 89 | ADP, MLT, AMP |
| 3 | 50 | 0.68 | 0.97 | 19 | empty |
| 4 | 50 | 0.68 | 0.97 | 19 | empty |
| 5 | 98 | 0.48 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1080 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1072 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1065 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 6DZG · Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q92SA6 · AlphaFold monomer V2.0 prediction for POLYPHOSPHATE:ADP phosphotransferase 1 (Q92SA6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q92SA6
- Elsewhere: RCSB PDB 6DZG · PDBe 6DZG · UniProt Q92SA6
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