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- PDB-9xwt: Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor -

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Basic information

Entry
Database: PDB / ID: 9xwt
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 / cytoplasm / cytosol
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: 2.28 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 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,16510
Polymers59,8342
Non-polymers1,3308
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-10 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.273, 83.114, 100.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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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

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-A1E1M / 7-bromanyl-5-chloranyl-1~{H}-indole-2-carboxylic acid


Mass: 274.499 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H5BrClNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / 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.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES 6.0, 8% PEG3350

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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: 2.28→50 Å / Num. obs: 29910 / % possible obs: 97 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Χ2: 0.792 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.28-2.3611.80.99729730.8290.9520.2941.0410.46798.4
2.36-2.4611.30.73229670.8750.9660.220.7660.47397.2
2.46-2.57120.56429150.9330.9830.1640.5880.47996.6
2.57-2.712.60.41529730.9650.9910.1180.4320.52697.7
2.7-2.8712.50.29729440.9820.9950.0840.3090.57696.4
2.87-3.0912.30.18729290.9890.9970.0540.1950.64795.8
3.09-3.4111.90.11628880.9950.9990.0340.1210.80794.5
3.41-3.912.60.07529900.99810.0210.0781.13496.2
3.9-4.9111.90.05230640.99910.0150.0541.40697.8
4.91-5012.30.04832670.99910.0140.0511.29699.3

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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: 2.28→49.77 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1497 5.04 %
Rwork0.1962 --
obs0.1989 29689 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 73 59 3953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083998
X-RAY DIFFRACTIONf_angle_d0.9515427
X-RAY DIFFRACTIONf_dihedral_angle_d8.762541
X-RAY DIFFRACTIONf_chiral_restr0.05566
X-RAY DIFFRACTIONf_plane_restr0.008701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.29431090.2422543X-RAY DIFFRACTION97
2.35-2.440.28371490.22952519X-RAY DIFFRACTION96
2.44-2.540.27931350.23662496X-RAY DIFFRACTION95
2.54-2.650.31741280.24752530X-RAY DIFFRACTION96
2.65-2.790.33461610.23752500X-RAY DIFFRACTION96
2.79-2.970.30111220.23182548X-RAY DIFFRACTION96
2.97-3.20.2981240.23242503X-RAY DIFFRACTION95
3.2-3.520.27111270.22172508X-RAY DIFFRACTION95
3.52-4.030.24321450.18872585X-RAY DIFFRACTION97
4.03-5.070.21751550.15712645X-RAY DIFFRACTION98
5.07-49.770.2051420.17512815X-RAY DIFFRACTION99

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