[English] 日本語
Yorodumi
- PDB-4gpd: THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gpd
TitleTHE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION
ComponentsAPO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(ALDEHYDE(D)-NAD(A))
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomarus americanus (American lobster)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGriffith, J.P. / Song, S. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1980
Title: Structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 A resolution.
Authors: Murthy, M.R. / Garavito, R.M. / Johnson, J.E. / Rossmann, M.G.
#1: Journal: J.Biol.Chem. / Year: 1975
Title: Studies of Asymmetry in the Three-Dimensional Structure of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Moras, D. / Olsen, K.W. / Sabesan, M.N. / Buehner, M. / Ford, G.C. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#4: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Rossmann, M.G.
#5: Journal: J.Biol.Chem. / Year: 1975
Title: Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Moras, D. / Rossmann, M.G. / Harris, J.I.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: D-Glyceraldehyde-3-Phosphate Dehydrogenase, Three-Dimensional Structure and Evolutionary Significance
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#9: Journal: Acta Crystallogr.,Sect.A / Year: 1975
Title: An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure
Authors: Argos, P. / Ford, G.C. / Rossmann, M.G.
History
DepositionJan 4, 1988Processing site: BNL
SupersessionJul 12, 1989ID: 2GPD
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE ...SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. STRANDS 1-7 OF SHEET C1 ARE IDENTICAL TO STRANDS 1-7 OF SHEET C2.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
2: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
3: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
4: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)143,0324
Polymers143,0324
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-54 kcal/mol
Surface area47470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.019, 80.956, 82.545
Angle α, β, γ (deg.)110.85, 71.47, 116.86
Int Tables number1
Space group name H-MP1
Atom site foot note1: SEE REMARK 6.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99755, 0.06825, 0.01534), (0.06743, 0.87985, 0.47044), (0.01861, 0.47033, -0.88232)103.10318, -20.02042, 64.92454
2given(-0.34281, 0.20463, -0.91685), (0.20517, -0.93612, -0.28564), (-0.91675, -0.28604, 0.27893)104.43578, 72.71724, 91.16001
3given(0.34413, -0.26927, 0.89948), (-0.27332, -0.94523, -0.1784), (0.89818, -0.18444, -0.39885)4.94277, 93.71841, 20.86403
DetailsTHE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 2 WHEN APPLIED TO CHAIN 1. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 3 WHEN APPLIED TO CHAIN 1. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 4 WHEN APPLIED TO CHAIN 1.

-
Components

#1: Protein
APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Mass: 35757.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homarus americanus (American lobster)
References: UniProt: P00357, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH SUBUNIT IS CONSIDERED TO BE COMPRISED OF A COFACTOR BINDING DOMAIN AND A CATALYTIC DOMAIN. THE ...EACH SUBUNIT IS CONSIDERED TO BE COMPRISED OF A COFACTOR BINDING DOMAIN AND A CATALYTIC DOMAIN. THE CHARACTERS B AND C IN THE SHEET IDENTIFIERS ARE USED TO DENOTE WHICH DOMAIN INCLUDES THESE STRUCTURAL FEATURES.
Sequence detailsTHE SEQUENCE GIVEN IN *PIR* SHOWS RESIDUE 6 TO BE ASP. THE DATA PRESENTED IN THIS ENTRY SHOWS ...THE SEQUENCE GIVEN IN *PIR* SHOWS RESIDUE 6 TO BE ASP. THE DATA PRESENTED IN THIS ENTRY SHOWS RESIDUE 6 AS ASN (M. ROSSMANN, PRIVATE COMMUNICATION FROM J. HARRIS).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal grow
*PLUS
Method: microdialysis / PH range low: 6.4 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein11
23.08 Mammonium sulfate12
31 mMEDTA12
41 mMdithiothreitol12
5chloroform12dialyzing medium

-
Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 30128 / % possible obs: 86 % / Num. measured all: 56899

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→6 Å / σ(I): 3
Details: THE PHASES FOR APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE WERE DERIVED BY THE MOLECULAR REPLACEMENT TECHNIQUE. THE INITIAL PHASING MODEL WAS THE HOLO GAPDH ELECTRON DENSITY SUITABLY ...Details: THE PHASES FOR APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE WERE DERIVED BY THE MOLECULAR REPLACEMENT TECHNIQUE. THE INITIAL PHASING MODEL WAS THE HOLO GAPDH ELECTRON DENSITY SUITABLY TRANSFORMED TO THE TRICLINIC APO GAPDH CELL. THE KNOWN 222 SYMMETRY OF THE TETRAMERIC MOLECULE WAS USED IN IMPROVING THE PHASES BY ELECTRON DENSITY AVERAGING. THE STRUCTURE WAS FOUND TO BE VERY SIMILAR TO THAT OF THE HOLO ENZYME.
RfactorNum. reflection
obs0.218 27016
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 0 122 10150
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / Num. reflection obs: 27016 / σ(I): 3 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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