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- PDB-5n53: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 5n53
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / serine metabolism / FBDD
Function / homology
Function and homology information


gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase ...gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase / L-serine biosynthetic process / L-malate dehydrogenase activity / G1 to G0 transition / neural tube development / spinal cord development / glutamine metabolic process / brain development / neuron projection development / NAD binding / 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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
~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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
DepositionFeb 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 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 1.2Jan 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)42,3034
Polymers41,9042
Non-polymers3992
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-31 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.353, 45.323, 55.255
Angle α, β, γ (deg.)97.900, 110.060, 106.350
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / 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: 0 / 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


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) / Variant (production host): Rosetta (DE3) / References: UniProt: O43175, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-8NB / ~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide


Mass: 199.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10ClNO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP, pH 7, 23-25 % 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: 1.48→50.12 Å / Num. obs: 51238 / % possible obs: 86.1 % / Redundancy: 2.13 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.1 / Net I/σ(I): 4.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.14 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2530 / CC1/2: 0.355 / Rpim(I) all: 0.972 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
xia20.3.8.0data reduction
xia20.3.8.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 1.48→50.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.83 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 2651 5.2 %RANDOM
Rwork0.1891 ---
obs0.1919 48587 84.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 19.681 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.47 Å20.68 Å2
2---0.58 Å21.25 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.48→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 26 238 3184
Biso mean--35.27 31.19 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193171
X-RAY DIFFRACTIONr_bond_other_d0.0070.023093
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9734304
X-RAY DIFFRACTIONr_angle_other_deg1.4122.9927147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19124.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76915569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4531523
X-RAY DIFFRACTIONr_chiral_restr0.1230.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213688
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02687
X-RAY DIFFRACTIONr_rigid_bond_restr4.37236264
X-RAY DIFFRACTIONr_sphericity_free36.748567
X-RAY DIFFRACTIONr_sphericity_bonded21.85356371
Refine LS restraints NCS

Ens-ID: 1 / Number: 23386 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.484→1.522 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 160 -
Rwork0.283 2891 -
all-3051 -
obs--68.1 %

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