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- PDB-1nhx: PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1nhx
TitlePEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR
ComponentsPHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC
KeywordsLYASE / GLUCONEOGENESIS / XANTHINE / INHIBITOR
Function / homology
Function and homology information


cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose ...cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / Gluconeogenesis / cellular hyperosmotic salinity response / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to insulin / Transcriptional regulation of white adipocyte differentiation / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-FTB / : / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / RIGID-BODY REFINEMENT / Resolution: 2.1 Å
AuthorsFoley, L.H. / Wang, P. / Dunten, P. / Ramsey, G. / Gubler, M.-L. / Wertheimer, S.J.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: X-RAY STRUCTURES OF TWO XANTHINE INHIBITORS BOUND TO PEPCK and N-3 modifications of substituted 1,8-Dibenzylxanthines
Authors: FOLEY, L.H. / WANG, P. / DUNTEN, P. / RAMSEY, G. / GUBLER, M.-L. / WERTHEIMER, S.J.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC PHOSPHOENOLPYRUVATE CARBOXYKINASE REVEALS A NEW GTP-BINDING SITE
Authors: DUNTEN, P. / BELUNIS, C. / CROWTHER, R. / HOLLFELDER, K. / KAMMLOTT, U. / LEVIN, W. / MICHEL, H. / RAMSEY, G.B. / SWAIN, A. / WEBER, D. / WERTHEIMER, S.J.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3637
Polymers69,5301
Non-polymers8346
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.383, 61.452, 62.265
Angle α, β, γ (deg.)89.71, 70.24, 72.56
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC / / Phosphoenolpyruvate carboxylase / PEPCK-C


Mass: 69529.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P35558, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 6 types, 298 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Chemical ChemComp-FTB / N-{4-[1-(2-FLUOROBENZYL)-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL]-PHENYL}-ACETAMIDE / 1-(2-FLUOROBENZYL)-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)-XANTHINE


Mass: 463.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26FN5O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 32199 / Num. obs: 32199 / % possible obs: 91.3 % / Redundancy: 2.2 % / Rsym value: 0.041 / Net I/σ(I): 23.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2 % / Rsym value: 0.083 / % possible all: 84
Reflection
*PLUS
Highest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: RIGID-BODY REFINEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.3 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.21718 1616 5 %RANDOM
Rwork0.17304 ---
obs0.17532 32191 91.52 %-
all-32191 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20.03 Å2-0.3 Å2
2--0.62 Å2-0.29 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 54 292 5081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214909
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9646647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955603
X-RAY DIFFRACTIONr_chiral_restr0.0770.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023744
X-RAY DIFFRACTIONr_nbd_refined0.1870.22312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2368
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.29
X-RAY DIFFRACTIONr_mcbond_it0.5191.53012
X-RAY DIFFRACTIONr_mcangle_it0.99124850
X-RAY DIFFRACTIONr_scbond_it1.55931897
X-RAY DIFFRACTIONr_scangle_it2.614.51797
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.274 106
Rwork0.187 2160
obs-2266
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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