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- PDB-5y35: Phosphoglycerate mutase 1 complexed with a small molecule inhibit... -

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Basic information

Entry
Database: PDB / ID: 5y35
TitlePhosphoglycerate mutase 1 complexed with a small molecule inhibitor KH1
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE/INHIBITOR / phosphoglycerate mutase 1 / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-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 / 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-8LF / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.994 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC21472026 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH1
Authors: Jiang, L.L. / Zhou, L.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)60,4745
Polymers59,8342
Non-polymers6403
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-6 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.836, 85.105, 103.046
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

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-8LF / ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-methyl-benzenesulfonamide


Mass: 409.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15NO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.04 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES, pH 6.0, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 47888 / % possible obs: 95.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.84 Å2 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.074 / Rrim(I) all: 0.173 / Χ2: 1.037 / Net I/σ(I): 6.1 / Num. measured all: 320116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.99-2.067.30.97449600.7380.3840.999100
2.06-2.147.30.7449350.8150.2921.0851000.796
2.14-2.246.40.55941610.9460.2411.07883.60.611
2.24-2.366.50.37241510.9540.1621.05383.60.407
2.36-2.517.30.31149610.9580.1231.0551000.334
2.51-2.77.30.24150000.9730.0961.0341000.26
2.7-2.977.20.18350010.9810.0741.0461000.198
2.97-3.46.70.1450430.9870.061.01199.80.153
3.4-4.295.10.10244270.9850.0511.03287.10.114
4.29-505.60.08352490.990.040.97798.80.093

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXphenix.refine: 1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPI

4gpi


Resolution: 1.994→43.751 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.57
RfactorNum. reflection% reflection
Rfree0.2439 2415 5.12 %
Rwork0.2162 --
obs0.2177 47158 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.69 Å2 / Biso mean: 34.04 Å2 / Biso min: 17.94 Å2
Refinement stepCycle: final / Resolution: 1.994→43.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 42 302 4126
Biso mean--52.63 36.71 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093931
X-RAY DIFFRACTIONf_angle_d1.2025341
X-RAY DIFFRACTIONf_chiral_restr0.049559
X-RAY DIFFRACTIONf_plane_restr0.007690
X-RAY DIFFRACTIONf_dihedral_angle_d14.7761476
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2197X-RAY DIFFRACTION6.518TORSIONAL
12C2197X-RAY DIFFRACTION6.518TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9939-2.03460.33071430.2592595273894
2.0346-2.07880.25491440.23727752919100
2.0788-2.12720.23861620.231227842946100
2.1272-2.18040.29271370.242827802917100
2.1804-2.23930.4452960.3621827192365
2.2393-2.30520.6486890.54211539162857
2.3052-2.37960.24811310.239228052936100
2.3796-2.46460.27911680.208427592927100
2.4646-2.56330.25711460.203228012947100
2.5633-2.680.22541540.202427822936100
2.68-2.82120.22611410.198428232964100
2.8212-2.99790.22311520.206327952947100
2.9979-3.22940.23691530.210128192972100
3.2294-3.55420.21261370.21328362973100
3.5542-4.06820.23511240.20192221234578
4.0682-5.12420.19371790.16352837301699
5.1242-43.76110.20481590.19932965312498

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