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Crystal structure of phosphoenolpyruvate carboxykinase (pepck) from trypanosoma cruzi
Analyse Crystal structure of phosphoenolpyruvate carboxykinase (pepck) from trypanosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1II2
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.32
- UniProt
- P51058
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase (EC 4.1.1.32) | protein | 522 | 32% helix, 25% strand | P51058 |
| B | Phosphoenolpyruvate carboxykinase (EC 4.1.1.32) | protein | 514 | 31% helix, 26% strand | P51058 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.72 | 0.80 | 50 | SO4 |
| 2 | 396 | 0.71 | 0.82 | 42 | SO4 |
| 3 | 233 | 0.65 | 0.83 | 49 | empty |
| 4 | 515 | 0.60 | 0.74 | 61 | empty |
| 5 | 163 | 0.53 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 582 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1II2 · Crystal Structure of Phosphoenolpyruvate Carboxykinase (PEPCK) from Trypanosoma cruzi · the same entry in another collection · chain A against A, TM-score 1.00
- P51058 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP), glycosomal… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P51058
- Elsewhere: RCSB PDB 1II2 · PDBe 1II2 · UniProt P51058
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