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- PDB-6cwa: CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERA... -

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Basic information

Entry
Database: PDB / ID: 6cwa
TitleCRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / PHGDH
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
3-PHOSPHOGLYCERIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsDavies, D.R. / Edwards, T.E.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis.
Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / ...Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / Zoephel, A. / Schnitzer, R. / Sommergruber, W. / Martinelli, P. / Arnhof, H. / Peric-Simov, B. / Hofbauer, K.S. / Garavel, G. / Scherbantin, Y. / Mitzner, S. / Fett, T.N. / Scholz, G. / Bruchhaus, J. / Burkard, M. / Kousek, R. / Ciftci, T. / Sharps, B. / Schrenk, A. / Harrer, C. / Haering, D. / Wolkerstorfer, B. / Zhang, X. / Lv, X. / Du, A. / Li, D. / Li, Y. / Quant, J. / Pearson, M. / McConnell, D.B.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: 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.title / _citation_author.name
Revision 1.2Oct 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,8146
Polymers70,1112
Non-polymers1,7034
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-49 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 59.620, 63.480
Angle α, β, γ (deg.)89.64, 89.83, 79.36
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35055.266 Da / Num. of mol.: 2 / Fragment: PHGDH
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-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 MM IMIDAZOLE PH 6.5, 20% PEG 3350, 100 MM MAGNESIUM CHLORIDE, 2M NACL, 1MM NADH; SOAK OVERNIGHT IN CRYSTALLIZATION SOLUTION PLUS 5 MM 3- PHOSPHOGLYCERATE; 20% EG CRYO, VAPOR DIFFUSION, TEMPERATURE 289K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.77→28.36 Å / Num. obs: 58407 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.65 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.19
Reflection shellResolution: 1.77→1.82 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXdev_1702refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 1.77→28.36 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.223 2904 4.97 %
Rwork0.192 --
obs0.193 58386 96.4 %
Solvent computationShrinkage radii: 0.9 Å
Displacement parametersBiso mean: 36.59 Å2
Refinement stepCycle: LAST / Resolution: 1.77→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 110 311 4465
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4904-0.4514-1.59791.08580.34913.3027-0.2662-0.5055-0.5920.6834-0.1690.52560.523-0.06120.35820.9837-0.01510.40960.787-0.00780.578-6.7179-11.178347.4667
22.6636-1.9485-0.16874.45861.24660.45990.0738-0.3639-0.07630.0492-0.34941-1.1483-0.08830.28790.9672-0.00490.11670.6705-0.20160.3548-6.66380.620944.7023
32.051-0.0294-0.10233.68650.27330.67110.1075-0.02470.2935-0.2486-0.0444-0.2193-0.0668-0.0254-0.04650.1059-0.00670.03790.1410.01210.14317.3301-4.418119.1066
42.7298-0.5407-0.72120.9313-1.52213.80390.01190.7625-0.2124-1.69790.28870.4406-0.4179-0.0862-0.18591.23350.02370.05450.7276-0.14110.306413.7521-30.7042-11.3486
51.83190.3338-0.06933.65510.51240.32950.0740.0681-0.2429-0.2558-0.035-0.1091-0.02150.0095-0.01050.1291-0.0002-0.00940.16290.00530.09644.7248-27.584115.757

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