[English] 日本語
Yorodumi
- PDB-5nzp: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nzp
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Hydroxybenzisoxazole
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / serine metabolism / FBDD
Function / homology
Function and homology information


threonine metabolic process / 2-oxoglutarate reductase / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process ...threonine metabolic process / 2-oxoglutarate reductase / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / neural tube development / spinal cord development / G1 to G0 transition / glutamine metabolic process / 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
1,2-benzoxazol-3-ol / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.1Apr 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 1.2May 8, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn / struct_conn_type
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,1254
Polymers43,8542
Non-polymers2702
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-32 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.362, 45.587, 55.353
Angle α, β, γ (deg.)97.23, 110.45, 106.72
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: 5 - 199

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

-
Components

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


Mass: 21927.199 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-9EW / 1,2-benzoxazol-3-ol


Mass: 135.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP, pH 7, 23-25 % PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 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: 1.3→50.2 Å / Num. obs: 75610 / % possible obs: 84.7 % / Redundancy: 1.95 % / Net I/σ(I): 4.5
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 1 / Num. unique obs: 3737 / CC1/2: 0.563 / Rpim(I) all: 0.622

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→50.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.221 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21604 3878 5.1 %RANDOM
Rwork0.17569 ---
obs0.17779 71726 83.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20.26 Å20.1 Å2
2---0.08 Å20.42 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.3→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 20 167 3107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193160
X-RAY DIFFRACTIONr_bond_other_d0.0090.023076
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9754288
X-RAY DIFFRACTIONr_angle_other_deg1.4912.9977109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61824.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97915569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7581523
X-RAY DIFFRACTIONr_chiral_restr0.1310.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213666
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02685
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0971.5791647
X-RAY DIFFRACTIONr_mcbond_other3.0451.5771646
X-RAY DIFFRACTIONr_mcangle_it3.7412.3682085
X-RAY DIFFRACTIONr_mcangle_other3.7652.372086
X-RAY DIFFRACTIONr_scbond_it4.1261.9631513
X-RAY DIFFRACTIONr_scbond_other4.1241.9651514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7792.8222204
X-RAY DIFFRACTIONr_long_range_B_refined4.88513.4833529
X-RAY DIFFRACTIONr_long_range_B_other4.88213.3633472
X-RAY DIFFRACTIONr_rigid_bond_restr5.75536236
X-RAY DIFFRACTIONr_sphericity_free22.755542
X-RAY DIFFRACTIONr_sphericity_bonded14.15856296
Refine LS restraints NCS

Ens-ID: 1 / Number: 23180 / 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: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 225 -
Rwork0.274 4117 -
obs--64.75 %

+
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