Research workbench
Crystal structure of polyphosphate kinase 2 from arthrobacter aurescens TC1
Analyse Crystal structure of polyphosphate kinase 2 from arthrobacter aurescens TC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RHF
- Type
- protein
- Length
- 1,124 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polyphosphate kinase 2 family protein
- UniProt
- A1R8G0
- Ligands
- PO4, CL
- Pockets
- 19 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative polyphosphate kinase 2 family protein | protein | 283 | 53% helix, 12% strand | A1R8G0 |
| B, C | Putative polyphosphate kinase 2 family protein | protein | 281 | 54% helix, 12% strand | A1R8G0 |
| D | Putative polyphosphate kinase 2 family protein | protein | 279 | 52% helix, 11% strand | A1R8G0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, D, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains B, D, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.64 | 0.79 | 42 | FLC, PO4 |
| 2 | 361 | 0.63 | 0.79 | 32 | FLC, PO4 |
| 3 | 408 | 0.63 | 0.78 | 40 | PO4 |
| 4 | 367 | 0.63 | 0.78 | 40 | FLC, PO4 |
| 5 | 432 | 0.61 | 0.76 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1976 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1941 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 715 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3RHF · Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1 · the same entry in another collection · chain B against B, 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 A1R8G0
- Elsewhere: RCSB PDB 3RHF · PDBe 3RHF · UniProt A1R8G0
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