Research workbench
Crystal structure of pichia pastoris phosphofructokinase in the T- state
Analyse Crystal structure of pichia pastoris phosphofructokinase in the T- state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OPY
- Type
- protein
- Length
- 8,572 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphofructo-1-kinase alpha-subunit; 6-phosphofructo-1-kinase beta-subunit…
- EC
- 2.7.1.11
- UniProt
- Q8NJU8, Q8TGA0, A7MAS3
- Ligands
- ATP, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | 6-phosphofructo-1-kinase alpha-subunit (EC 2.7.1.11) | protein | 936 | 38% helix, 20% strand | Q8NJU8 |
| B, D, F, H | 6-phosphofructo-1-kinase beta-subunit (EC 2.7.1.11) | protein | 884 | 42% helix, 17% strand | Q8TGA0 |
| I, J, K, L | 6-phosphofructo-1-kinase gamma-subunit (EC 2.7.1.11) | protein | 323 | 47% helix, 19% strand | A7MAS3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains F, D, B, H
- SO4 · Sulfate ion · ion · 65 copies · chains A, B, E, F, I, C, D, J, G, H, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.86 | 0.87 | 141 | SO4 |
| 2 | 917 | 0.85 | 0.86 | 93 | SO4 |
| 3 | 958 | 0.85 | 0.86 | 95 | empty |
| 4 | 936 | 0.85 | 0.86 | 108 | SO4 |
| 5 | 1024 | 0.85 | 0.85 | 90 | SO4 |
Interfaces
28 interfaces between chains.
- E–F · 3575 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 3574 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3567 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3548 Ų buried · 46 hydrogen bonds · protein-protein
- F–G · 2691 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3OPY · Crystal structure of Pichia pastoris phosphofructokinase in the T-state · the same entry in another collection · chain L against L, 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 Q8NJU8
- Every structure of UniProt Q8TGA0
- Every structure of UniProt A7MAS3
- Elsewhere: RCSB PDB 3OPY · PDBe 3OPY · UniProt Q8NJU8 · UniProt Q8TGA0 · UniProt A7MAS3
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