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
- 2PC9
- Type
- protein
- Length
- 2,055 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase [ATP]
- EC
- 4.1.1.49
- UniProt
- Q5SLL5
- Ligands
- ATP, CA, PO4
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) | protein | 515 | 30% helix, 25% strand | Q5SLL5 |
| B | Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) | protein | 511 | 30% helix, 26% strand | Q5SLL5 |
| C | Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) | protein | 517 | 32% helix, 25% strand | Q5SLL5 |
| D | Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) | protein | 512 | 31% helix, 26% strand | Q5SLL5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.81 | 0.83 | 127 | PO4, ATP |
| 2 | 1159 | 0.81 | 0.82 | 107 | ATP |
| 3 | 877 | 0.74 | 0.78 | 75 | PO4, ATP |
| 4 | 495 | 0.70 | 0.80 | 62 | PO4, ATP |
| 5 | 705 | 0.68 | 0.76 | 40 | PO4 |
Interfaces
3 interfaces between chains.
- C–D · 744 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 722 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2PC9 · Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus… · the same entry in another collection · chain D against D, 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 2PC9 · PDBe 2PC9 · UniProt Q5SLL5
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