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- PDB-7va1: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 7va1
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase in complex with GDD-04-35
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


2-oxoglutarate reductase / threonine metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / gamma-aminobutyric acid metabolic process / Serine metabolism / glycine metabolic process / malate dehydrogenase ...2-oxoglutarate reductase / threonine metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / 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 1 / 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 dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
Chem-5YP / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsCen, Y. / Gao, D. / Zhou, J. / Tian, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of Novel Drug-like PHGDH Inhibitors to Disrupt Serine Biosynthesis for Cancer Therapy.
Authors: Gao, D. / Tang, S. / Cen, Y. / Yuan, L. / Lan, X. / Li, Q.H. / Lin, G.Q. / Huang, M. / Tian, P.
History
DepositionAug 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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
C: D-3-phosphoglycerate dehydrogenase
D: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8288
Polymers91,8464
Non-polymers1,9824
Water6,882382
1
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4572
Polymers22,9611
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4572
Polymers22,9611
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4572
Polymers22,9611
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4572
Polymers22,9611
Non-polymers4961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.410, 112.520, 87.520
Angle α, β, γ (deg.)90.000, 92.358, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNILEILE(chain 'A' and (resid 102 through 114 or resid 116...AB102 - 1149 - 21
12CYSCYSARGARG(chain 'A' and (resid 102 through 114 or resid 116...AB116 - 15823 - 65
13VALVALVALVAL(chain 'A' and (resid 102 through 114 or resid 116...AB16067
14ARGARGGLUGLU(chain 'A' and (resid 102 through 114 or resid 116...AB163 - 29070 - 197
21ASNASNILEILE(chain 'B' and (resid 102 through 114 or resid 116...BA102 - 1149 - 21
22CYSCYSARGARG(chain 'B' and (resid 102 through 114 or resid 116...BA116 - 15823 - 65
23VALVALVALVAL(chain 'B' and (resid 102 through 114 or resid 116...BA16067
24ARGARGGLUGLU(chain 'B' and (resid 102 through 114 or resid 116...BA163 - 29070 - 197
31ASNASNILEILE(chain 'C' and (resid 102 through 114 or resid 116...CC102 - 1149 - 21
32CYSCYSARGARG(chain 'C' and (resid 102 through 114 or resid 116...CC116 - 15823 - 65
33VALVALVALVAL(chain 'C' and (resid 102 through 114 or resid 116...CC16067
34ARGARGGLUGLU(chain 'C' and (resid 102 through 114 or resid 116...CC163 - 29070 - 197
41ASNASNILEILE(chain 'D' and (resid 102 through 114 or resid 116...DD102 - 1149 - 21
42CYSCYSARGARG(chain 'D' and (resid 102 through 114 or resid 116...DD116 - 15823 - 65
43VALVALVALVAL(chain 'D' and (resid 102 through 114 or resid 116...DD16067
44ARGARGGLUGLU(chain 'D' and (resid 102 through 114 or resid 116...DD163 - 29070 - 197

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Components

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


Mass: 22961.391 Da / Num. of mol.: 4
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-5YP / 4-[(3-ethanoylphenyl)sulfamoyl]-~{N}-[4-(3-fluorophenyl)-1,3-thiazol-2-yl]benzamide


Mass: 495.546 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C24H18FN3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dihydrate 0.1 M Tris 8.0 20 %(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.74→47.31 Å / Num. obs: 85574 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.88 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.6
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 4491

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 1.74→43.37 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 4312 5.05 %
Rwork0.1964 81075 -
obs0.1979 85387 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.89 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 136 382 6247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616023
X-RAY DIFFRACTIONf_angle_d0.85868162
X-RAY DIFFRACTIONf_chiral_restr0.0545916
X-RAY DIFFRACTIONf_plane_restr0.00531065
X-RAY DIFFRACTIONf_dihedral_angle_d22.46652226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.37721370.35292650X-RAY DIFFRACTION99.82
1.76-1.780.35171370.34492729X-RAY DIFFRACTION99.62
1.78-1.80.39071300.33312724X-RAY DIFFRACTION99.96
1.8-1.820.33621570.32452687X-RAY DIFFRACTION99.58
1.83-1.850.30551280.31442705X-RAY DIFFRACTION99.72
1.85-1.870.32161620.28852709X-RAY DIFFRACTION99.51
1.87-1.90.3631420.28092685X-RAY DIFFRACTION99.75
1.9-1.930.311450.2652668X-RAY DIFFRACTION99.61
1.93-1.960.27211400.25272719X-RAY DIFFRACTION99.48
1.96-1.990.30621400.25052705X-RAY DIFFRACTION99.58
1.99-2.030.27541210.2342725X-RAY DIFFRACTION99.68
2.03-2.060.31031460.22562706X-RAY DIFFRACTION99.27
2.06-2.10.25991570.22642639X-RAY DIFFRACTION99.54
2.1-2.150.2551560.21032711X-RAY DIFFRACTION99.48
2.15-2.190.26381520.2032725X-RAY DIFFRACTION99.83
2.19-2.240.25661430.20172702X-RAY DIFFRACTION99.61
2.24-2.30.221530.19092705X-RAY DIFFRACTION99.65
2.3-2.360.23751460.20152681X-RAY DIFFRACTION99.72
2.36-2.430.24271430.20352702X-RAY DIFFRACTION99.79
2.43-2.510.26371340.19462717X-RAY DIFFRACTION99.58
2.51-2.60.24741590.20532687X-RAY DIFFRACTION99.58
2.6-2.70.27331430.19552715X-RAY DIFFRACTION99.44
2.7-2.830.21541300.20332711X-RAY DIFFRACTION99.61
2.83-2.980.23481380.20842697X-RAY DIFFRACTION99.23
2.98-3.160.23321370.2012718X-RAY DIFFRACTION99.34
3.16-3.410.21751500.20212714X-RAY DIFFRACTION99.41
3.41-3.750.18641600.16622687X-RAY DIFFRACTION99.2
3.75-4.290.17131640.15582716X-RAY DIFFRACTION99.34
4.29-5.40.18321250.15192721X-RAY DIFFRACTION98.85
5.4-43.370.15241370.16532715X-RAY DIFFRACTION97.24
Refinement TLS params.Method: refined / Origin x: -0.753215216874 Å / Origin y: -15.9631664874 Å / Origin z: 16.855423797 Å
111213212223313233
T0.227380840093 Å20.00511431186217 Å20.0287743974561 Å2-0.209889646554 Å20.00508151493407 Å2--0.287997463968 Å2
L0.421286222349 °20.0516305617182 °20.2494281292 °2-0.150014416764 °20.1242753673 °2--0.42275704548 °2
S-0.00907979407007 Å °0.00738977218038 Å °-0.088738929365 Å °-0.00563774742592 Å °-0.00606285713481 Å °-0.0214244501313 Å °0.0150003096353 Å °-0.00157350852058 Å °0.0102863801052 Å °
Refinement TLS groupSelection details: all

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