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- PDB-5y65: Phosphoglycerate mutase 1 complexed with a small molecule inhibit... -

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Basic information

Entry
Database: PDB / ID: 5y65
TitlePhosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2
Components(Phosphoglycerate mutase ...) x 2
KeywordsISOMERASE/INHIBITOR / phosphoglycerate mutase / ISOMERASE-INHIBITOR complex
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 / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HKB / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.554 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21472026 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2
Authors: Jiang, L.L. / Zhou, L.
History
DepositionAug 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)60,5825
Polymers59,9132
Non-polymers6693
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-9 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.193, 82.929, 99.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and segid B
21chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and segid BB0
211chain C and segid CC0

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Components

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Phosphoglycerate mutase ... , 2 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.: 1
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
#2: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29996.076 Da / Num. of mol.: 1
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 , 4 types, 57 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: 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
#5: Chemical ChemComp-HKB / ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-(dimethylamino)benzenesulfonamide


Mass: 438.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N2O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES pH 6.0, 8%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 21841 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 51.43 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.048 / Rrim(I) all: 0.119 / Χ2: 1.163 / Net I/σ(I): 6.8 / Num. measured all: 133070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.646.10.74421280.8120.3220.8130.47999.9
2.64-2.756.20.56121470.8610.2430.6130.54799.5
2.75-2.876.10.41621630.9060.1820.4550.57399.5
2.87-3.026.10.30821540.9390.1350.3370.65999.4
3.02-3.215.70.21621340.9670.0990.2380.86199.1
3.21-3.4660.16421720.9790.0720.181.0698.8
3.46-3.816.40.11721690.990.050.1281.50699.2
3.81-4.366.30.08921970.9920.0390.0982.09499.5
4.36-5.4960.07322210.9940.0330.082.08599.8
5.49-5060.05723560.9970.0250.0631.63499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.55 Å49.9 Å
Translation2.55 Å49.9 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.554→49.898 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.96
RfactorNum. reflection% reflection
Rfree0.248 1116 5.12 %
Rwork0.1975 --
obs0.2001 21790 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.18 Å2 / Biso mean: 34.57 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: final / Resolution: 2.554→49.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 44 54 3906
Biso mean--49.86 31.11 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093959
X-RAY DIFFRACTIONf_angle_d1.2375380
X-RAY DIFFRACTIONf_chiral_restr0.047561
X-RAY DIFFRACTIONf_plane_restr0.007694
X-RAY DIFFRACTIONf_dihedral_angle_d15.5361494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2100X-RAY DIFFRACTION11.341TORSIONAL
12C2100X-RAY DIFFRACTION11.341TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.554-2.67030.35331240.25525442668100
2.6703-2.8110.27771410.22862531267299
2.811-2.98710.32781320.223725522684100
2.9871-3.21770.26421410.22032554269599
3.2177-3.54150.28811550.21262546270199
3.5415-4.05370.25451410.18792569271099
4.0537-5.10650.19841320.16926472779100
5.1065-49.9080.21991500.19142731288199

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