Research workbench
Pepck complex with a GTP-competitive inhibitor
Analyse Pepck complex with a GTP-competitive inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NHX
- Type
- protein
- Length
- 605 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic
- EC
- 4.1.1.32
- UniProt
- P35558
- Ligands
- PEP, FTB, MN, NA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic (EC 4.1.1.32) | protein | 605 | 31% helix, 24% strand | P35558 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- FTB · N-{4-[1-(2-fluorobenzyl)-3-butyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-ylmethyl]-phenyl}-acetamide · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.72 | 0.81 | 61 | MN, NA, PEP, FTB |
| 2 | 143 | 0.56 | 0.82 | 22 | empty |
| 3 | 121 | 0.45 | 0.78 | 27 | empty |
| 4 | 54 | 0.38 | 0.80 | 18 | empty |
| 5 | 57 | 0.35 | 0.78 | 16 | empty |
Compared structures
- 1NHX · Pepck complex with a GTP-competitive inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P35558 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase, cytosolic [GTP]… · a predicted model of the same protein · 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 P35558
- Elsewhere: RCSB PDB 1NHX · PDBe 1NHX · UniProt P35558
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