MolNFT v1 · #60702 · protein
Crystal structure of putative polyphosphate kinase 2 from sinorhizobium meliloti
3CZQ: “Crystal structure of putative polyphosphate kinase 2 from sinorhizobium meliloti”. X-ray diffraction, 7 pockets (best druggability 0.84). MolNFT v1 #60702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CZQ
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polyphosphate kinase 2
- UniProt
- Q92SA6
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative polyphosphate kinase 2 | protein | 288 | 47% helix, 15% strand | Q92SA6 |
| B | Putative polyphosphate kinase 2 | protein | 287 | 48% helix, 15% strand | Q92SA6 |
| C | Putative polyphosphate kinase 2 | protein | 284 | 45% helix, 14% strand | Q92SA6 |
| D | Putative polyphosphate kinase 2 | protein | 286 | 46% helix, 14% strand | Q92SA6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.84 | 0.85 | 122 | FMT |
| 2 | 859 | 0.83 | 0.85 | 97 | GOL |
| 3 | 88 | 0.48 | 0.82 | 22 | empty |
| 4 | 89 | 0.48 | 0.82 | 22 | empty |
| 5 | 51 | 0.46 | 0.85 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1050 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1041 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 889 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 886 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 125 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3CZQ · Crystal structure of putative polyphosphate kinase 2 from Sinorhizobium meliloti · the same entry in another collection · chain D against D, TM-score 1.00
- Q92SA6 · AlphaFold monomer V2.0 prediction for POLYPHOSPHATE:ADP phosphotransferase 1 (Q92SA6) · a predicted model of the same protein · chain C 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 3CZQ · PDBe 3CZQ · UniProt Q92SA6
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