[English] 日本語
Yorodumi
- PDB-9xvs: Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xvs
TitlePhosphoglycerate mutase 1 complexed with a novel scaffold inhibitor
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE / PGAM1 / Inhibitor
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
: / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLi, S. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21TQ016 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor
Authors: Li, S. / Zhou, L.
History
DepositionNov 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Phosphoglycerate mutase 1
C: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,33114
Polymers59,8342
Non-polymers1,49712
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-13 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.807, 83.844, 103.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules BC

#1: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29917.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase

-
Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-A1E1K / 6-chloranyl-10-oxidanylidene-1,9-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4(13),5,7-tetraene-2-carboxylic acid


Mass: 264.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES 6.0, 8% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 42958 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.033 / Rrim(I) all: 0.118 / Χ2: 1.386 / Net I/σ(I): 5.1 / Num. measured all: 539769
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.1212.20.91342290.9250.980.2650.9520.52899.8
2.12-2.2112.70.68342390.9610.990.1960.7110.591100
2.21-2.3112.70.47442450.9790.9950.1370.4930.666100
2.31-2.4312.10.36942480.9770.9940.110.3850.78799.2
2.43-2.5813.30.27742160.9890.9970.0780.2880.93299.4
2.58-2.7813.20.20442770.9910.9980.0580.2121.249100
2.78-3.0612.80.15843040.9940.9980.0460.1651.695100
3.06-3.5112.50.11643040.9960.9990.0340.1212.32799.5
3.51-4.4212.20.08943620.9970.9990.0260.0932.88399.9
4.42-50120.0745340.99810.0210.0732.1899.3

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPI

4gpi


Resolution: 2.08→43.96 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 2023 4.75 %
Rwork0.2052 --
obs0.2069 42561 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 97 78 4036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084051
X-RAY DIFFRACTIONf_angle_d0.9865485
X-RAY DIFFRACTIONf_dihedral_angle_d12.333562
X-RAY DIFFRACTIONf_chiral_restr0.051569
X-RAY DIFFRACTIONf_plane_restr0.009705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.37911020.32842110X-RAY DIFFRACTION72
2.13-2.190.36251430.28042903X-RAY DIFFRACTION98
2.19-2.260.2861580.2482886X-RAY DIFFRACTION98
2.26-2.330.26461490.22572878X-RAY DIFFRACTION99
2.33-2.410.25821460.22892934X-RAY DIFFRACTION99
2.41-2.510.29951450.23662856X-RAY DIFFRACTION97
2.51-2.620.32171410.25092947X-RAY DIFFRACTION99
2.62-2.760.29741510.24912936X-RAY DIFFRACTION100
2.76-2.930.28071460.24952935X-RAY DIFFRACTION100
2.93-3.160.2821540.24022969X-RAY DIFFRACTION100
3.16-3.480.25731470.23352995X-RAY DIFFRACTION99
3.48-3.980.22621400.19073001X-RAY DIFFRACTION100
3.98-5.010.19261680.15932997X-RAY DIFFRACTION99
5.01-43.960.18881330.17033191X-RAY DIFFRACTION99

+
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