Research workbench
Crystal structure of ATP-dependent phosphoenolpyruvate carboxykinase from thermus thermophilus HB8
Analyse Crystal structure of ATP-dependent phosphoenolpyruvate carboxykinase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J3B
- Type
- protein
- Length
- 1,031 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent phosphoenolpyruvate carboxykinase
- UniProt
- Q7SIC6
- Ligands
- CA, PO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent phosphoenolpyruvate carboxykinase | protein | 513 | 32% helix, 26% strand | Q7SIC6 |
| B | ATP-dependent phosphoenolpyruvate carboxykinase | protein | 518 | 32% helix, 25% strand | Q7SIC6 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.77 | 0.79 | 88 | PO4 |
| 2 | 641 | 0.72 | 0.79 | 67 | PO4 |
| 3 | 539 | 0.68 | 0.78 | 52 | PO4 |
| 4 | 152 | 0.55 | 0.81 | 26 | CA, PO4 |
| 5 | 136 | 0.53 | 0.81 | 23 | CA, PO4 |
Interfaces
1 interface between chains.
- A–B · 1060 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1J3B · Crystal structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus… · 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 Q7SIC6
- Elsewhere: RCSB PDB 1J3B · PDBe 1J3B · UniProt Q7SIC6
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