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The structure of rat cytosolic pepck in complex with beta- sulfopyruvate and GTP

Analyse The structure of rat cytosolic pepck in complex with beta- sulfopyruvate and GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DT7
Type: protein
Length: 1,235 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
EC: 4.1.1.32
UniProt: P07379
Ligands: GTP, SPV, ETX, MN, NA
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32)	protein	624	30% helix, 23% strand	P07379
B	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32)	protein	611	31% helix, 23% strand	P07379

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
SPV · Sulfopyruvate · ligand · 2 copies · chains A, B
ETX · 2-ethoxyethanol · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 5 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
1PE · Pentaethylene glycol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.81	0.82	93	empty
2	361	0.69	0.82	51	MN, GTP, SPV
3	390	0.69	0.81	53	MN, GTP, SPV
4	201	0.60	0.81	27	empty
5	147	0.58	0.82	20	empty

Interfaces

1 interface between chains.

A–B · 498 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3DT7 · The structure of rat cytosolic PEPCK in complex with beta-sulfopyruvate and GTP · the same entry in another collection · chain A against A, TM-score 1.00
P07379 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase, cytosolic [GTP]… · a predicted model of the same protein · chain B 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 P07379
Elsewhere: RCSB PDB 3DT7 · PDBe 3DT7 · UniProt P07379

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