Research workbench
2.3A crystal structure of E. COLI phosphoenolpyruvate carboxykinase mutant ASP269ASN
Analyse 2.3A crystal structure of E. COLI phosphoenolpyruvate carboxykinase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6COM
- Type
- protein
- Length
- 526 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase (ATP)
- EC
- 4.1.1.49
- UniProt
- P22259
- Ligands
- ATP, PYR, CA, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase (ATP) (EC 4.1.1.49) | protein | 526 | 31% helix, 25% strand | P22259 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- PYR · Pyruvic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.73 | 0.80 | 70 | ATP, PYR, CA, MG |
| 2 | 103 | 0.39 | 0.76 | 21 | empty |
| 3 | 53 | 0.27 | 0.74 | 12 | empty |
Compared structures
- 6COM · 2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn · the same entry in another collection · chain A against A, TM-score 1.00
- P22259 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP) (P22259) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P22259
- Elsewhere: RCSB PDB 6COM · PDBe 6COM · UniProt P22259
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