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Crystal structure of pyrophosphate-dependent phosphofructokinase from marinobacter aquaeolei, northeast structural genomics consortium target MQR88
Analyse Crystal structure of pyrophosphate-dependent phosphofructokinase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K2Q
- Type
- protein
- Length
- 1,176 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrophosphate-dependent phosphofructokinase
- EC
- 2.7.1.90
- UniProt
- A1U3A9
- Ligands
- NA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pyrophosphate-dependent phosphofructokinase (EC 2.7.1.90) | protein | 392 | 39% helix, 19% strand | A1U3A9 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.71 | 0.79 | 49 | empty |
| 2 | 523 | 0.66 | 0.77 | 61 | NA |
| 3 | 506 | 0.65 | 0.77 | 69 | NA |
| 4 | 391 | 0.65 | 0.79 | 42 | empty |
| 5 | 384 | 0.63 | 0.78 | 45 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2493 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 288 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3K2Q · Crystal structure of Pyrophosphate-dependent phosphofructokinase from Marinobacter… · 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 A1U3A9
- Elsewhere: RCSB PDB 3K2Q · PDBe 3K2Q · UniProt A1U3A9
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