[English] 日本語
Yorodumi
- PDB-6cwa: CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERA... -

+
Open data


ID or keywords:

Loading...

-
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


threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / gamma-aminobutyric acid metabolic process / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase ...threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / gamma-aminobutyric acid metabolic process / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / 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 / 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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more