MolNFT v1 · #174156 · protein
Crystal structure of polyphosphate kinase 2 from deinococcus radiodurans in apo form
7BMM · PPK2 domain-containing protein: “Crystal structure of polyphosphate kinase 2 from deinococcus radiodurans in apo form”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.83). MolNFT v1 #174156 on GenesisL1: 3D…
- PDB
- 7BMM
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PPK2 domain-containing protein
- EC
- 2.7.4.1
- UniProt
- Q9RY20
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | PPK2 domain-containing protein (EC 2.7.4.1) | protein | 266 | 55% helix, 12% strand | Q9RY20 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.83 | 0.84 | 101 | empty |
| 2 | 648 | 0.73 | 0.80 | 76 | GOL, PO4 |
| 3 | 413 | 0.72 | 0.83 | 53 | GOL |
| 4 | 263 | 0.66 | 0.82 | 41 | empty |
| 5 | 273 | 0.65 | 0.82 | 34 | PO4 |
Interfaces
6 interfaces between chains.
- B–C · 1556 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1537 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1022 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 990 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BMM · Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form · the same entry in another collection · 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 Q9RY20
- Elsewhere: RCSB PDB 7BMM · PDBe 7BMM · UniProt Q9RY20
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