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
- 1XKV
- Type
- protein
- Length
- 1,034 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.49
- UniProt
- Q5SLL5
- Ligands
- ATP, CA, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent phosphoenolpyruvate carboxykinase (EC 4.1.1.49) | protein | 515 | 32% helix, 26% strand | Q5SLL5 |
| B | ATP-dependent phosphoenolpyruvate carboxykinase (EC 4.1.1.49) | protein | 519 | 31% helix, 24% strand | Q5SLL5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.76 | 0.78 | 104 | PO4, GOL |
| 2 | 702 | 0.73 | 0.79 | 68 | ATP |
| 3 | 776 | 0.72 | 0.77 | 71 | empty |
| 4 | 152 | 0.54 | 0.80 | 25 | CA, PO4 |
| 5 | 150 | 0.53 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1XKV · Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SLL5 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP) (Q5SLL5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5SLL5
- Elsewhere: RCSB PDB 1XKV · PDBe 1XKV · UniProt Q5SLL5
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