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- PDB-5nzo: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 5nzo
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / serine metabolism / FBDD
Function / homology
Function and homology information


2-oxoglutarate reductase / threonine metabolic process / glial cell development / taurine metabolic process / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / gamma-aminobutyric acid metabolic process / Serine metabolism / glycine metabolic process / malate dehydrogenase ...2-oxoglutarate reductase / threonine metabolic process / glial cell development / taurine metabolic process / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / gamma-aminobutyric acid metabolic process / Serine metabolism / glycine metabolic process / malate dehydrogenase / L-serine biosynthetic process / L-malate dehydrogenase (NAD+) activity / glutamine metabolic process / G1 to G0 transition / neural tube development / spinal cord development / brain development / NAD binding / neuron projection development / regulation of gene expression / electron transfer activity / extracellular exosome / cytosol
Similarity search - Function
D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-methyl-5-phenyl-pyrazol-3-amine / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsUnterlass, J.E. / Basle, A. / Blackburn, T.J. / Tucker, J. / Cano, C. / Noble, M.E.M. / Curtin, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: Oncotarget / Year: 2018
Title: Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
Authors: Unterlass, J.E. / Basle, A. / Blackburn, T.J. / Tucker, J. / Cano, C. / Noble, M.E.M. / Curtin, N.J.
History
DepositionMay 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name
Revision 1.3Feb 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: D-3-phosphoglycerate dehydrogenase
A: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2514
Polymers41,9042
Non-polymers3462
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-31 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.391, 45.783, 54.807
Angle α, β, γ (deg.)97.050, 110.120, 106.650
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 100 - 294 / Label seq-ID: 1 - 195

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein D-3-phosphoglycerate dehydrogenase / 3-PGDH / 2-oxoglutarate reductase / Malate dehydrogenase


Mass: 20952.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Production host: Escherichia coli (E. coli)
References: UniProt: O43175, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, malate dehydrogenase
#2: Chemical ChemComp-9EZ / 2-methyl-5-phenyl-pyrazol-3-amine


Mass: 173.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP buffer, pH 7 and 23-28 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.29→49.9 Å / Num. obs: 73976 / % possible obs: 82.8 % / Redundancy: 1.94 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 4
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.917 / Num. unique all: 3742 / CC1/2: 0.352 / % possible all: 84.2

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 1.29→49.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.366 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 3651 4.9 %RANDOM
Rwork0.1963 ---
obs0.1984 70307 79.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.43 Å2 / Biso mean: 20.254 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.79 Å2-0.2 Å2
2---0.2 Å21.68 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.29→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 26 272 3218
Biso mean--30.34 32.54 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193173
X-RAY DIFFRACTIONr_bond_other_d0.0080.023095
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9714308
X-RAY DIFFRACTIONr_angle_other_deg1.4672.9927149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61924.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36215569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7251523
X-RAY DIFFRACTIONr_chiral_restr0.1320.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213690
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02695
X-RAY DIFFRACTIONr_rigid_bond_restr4.26136268
X-RAY DIFFRACTIONr_sphericity_free38.383569
X-RAY DIFFRACTIONr_sphericity_bonded19.94356405
Refine LS restraints NCS

Ens-ID: 1 / Number: 23218 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.286→1.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 119 -
Rwork0.328 2316 -
all-2435 -
obs--35.11 %

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