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- PDB-4o33: Crystal Structure of human PGK1 3PG and terazosin(TZN) ternary complex -

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Basic information

Entry
Database: PDB / ID: 4o33
TitleCrystal Structure of human PGK1 3PG and terazosin(TZN) ternary complex
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / ENZYME-DRUG COMPLEX / TRANSFERASE-TRANSFERASE ACTIVITOR complex / TRANSFERASE-TRANSFERASE ACTIVATOR complex
Function / homology
Function and homology information


Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / extracellular space / extracellular exosome / ATP binding / membrane / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Chem-TZN / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, X.L. / Finci, L.I. / Wang, J.H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Terazosin activates Pgk1 and Hsp90 to promote stress resistance.
Authors: Chen, X. / Zhao, C. / Li, X. / Wang, T. / Li, Y. / Cao, C. / Ding, Y. / Dong, M. / Finci, L. / Wang, J.H. / Li, X. / Liu, L.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2343
Polymers44,6611
Non-polymers5732
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.817, 73.754, 93.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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Components

#1: Protein Phosphoglycerate kinase 1 / Cell migration-inducing gene 10 protein / Primer recognition protein 2 / PRP 2


Mass: 44660.566 Da / Num. of mol.: 1 / Fragment: protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1, PGKA, MIG10, OK/SW-cl.110 / Production host: Escherichia coli (E. coli) / References: UniProt: P00558, phosphoglycerate kinase
#2: Chemical ChemComp-TZN / [4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piperazin-1-yl][(2R)-tetrahydrofuran-2-yl]methanone / Terazosin


Mass: 387.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N5O4 / Comment: medication*YM
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 291 K / pH: 8
Details: 25-30% PEG 4000,0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291 KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24406 / % possible obs: 90 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.13→2.17 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XE6

2xe6


Resolution: 2.1→34.3 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1998 8.19 %
Rwork0.193 --
obs0.196 24391 95.9 %
all-2160 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 39 308 3470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163213
X-RAY DIFFRACTIONf_angle_d1.3434333
X-RAY DIFFRACTIONf_dihedral_angle_d15.2551210
X-RAY DIFFRACTIONf_chiral_restr0.088492
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1051-2.15780.30611180.23351327X-RAY DIFFRACTION81
2.1578-2.21610.28951460.25071635X-RAY DIFFRACTION100
2.2161-2.28130.33891370.26691548X-RAY DIFFRACTION93
2.2813-2.35490.23581450.22581620X-RAY DIFFRACTION100
2.3549-2.4390.25451470.20061648X-RAY DIFFRACTION100
2.439-2.53670.25121480.22411658X-RAY DIFFRACTION100
2.5367-2.65210.28581460.22071626X-RAY DIFFRACTION100
2.6521-2.79180.24951480.2221661X-RAY DIFFRACTION100
2.7918-2.96670.24271480.21871664X-RAY DIFFRACTION100
2.9667-3.19560.22531480.20611657X-RAY DIFFRACTION99
3.1956-3.51690.21191470.1861638X-RAY DIFFRACTION98
3.5169-4.02510.19851230.17021393X-RAY DIFFRACTION83
4.0251-5.06860.15341430.15831591X-RAY DIFFRACTION93
5.0686-34.30810.19041540.15731727X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -1.0959 Å / Origin y: 17.133 Å / Origin z: 21.9244 Å
111213212223313233
T0.1413 Å20.0122 Å2-0.0113 Å2-0.1475 Å20.0011 Å2--0.1373 Å2
L0.4562 °20.1073 °2-0.3668 °2-0.1581 °2-0.0207 °2--0.4434 °2
S0.0156 Å °-0.0305 Å °0.0103 Å °0.0141 Å °-0.0241 Å °-0.0278 Å °-0.0239 Å °-0.0001 Å °0 Å °
Refinement TLS groupSelection details: all

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