[English] 日本語
Yorodumi
- PDB-4o33: Crystal Structure of human PGK1 3PG and terazosin(TZN) ternary complex -

+
Open data


ID or keywords:

Loading...

-
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 / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / ADP binding / gluconeogenesis / glycolytic process / cellular response to hypoxia / membrane raft / phosphorylation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / 3-Phosphoglyceric acid


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


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more