[English] 日本語
Yorodumi
- PDB-3gpd: TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gpd
TitleTWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (NAD(A)-ALDEHYDE(D))
Function / homology
Function and homology information


peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / vesicle / killing of cells of another organism / protein stabilization / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsWatson, H.C. / Campbell, J.C.
Citation
Journal: J.Mol.Biol. / Year: 1976
Title: Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase.
Authors: Mercer, W.D. / Winn, S.I. / Watson, H.C.
#1: Journal: Nature New Biol. / Year: 1972
Title: Low Resolution Structure of Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Watson, H.C. / Duee, E. / Mercer, W.D.
#2: Journal: FEBS Lett. / Year: 1981
Title: The Complete Amino Acid Sequence of Human Muscle Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Nowak, K. / Wolny, M. / Banas, T.
History
DepositionJun 20, 1983Processing site: BNL
Revision 1.0Oct 27, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET EACH SUBUNIT HAS A COFACTOR-BINDING DOMAIN AND A CATALYTIC DOMAIN. FOLLOWING THE NOMENCLATURE ...SHEET EACH SUBUNIT HAS A COFACTOR-BINDING DOMAIN AND A CATALYTIC DOMAIN. FOLLOWING THE NOMENCLATURE USED IN THE LOBSTER AND BACILLUS STEAROTHERMOPHILUS ENTRIES, THE LETTERS B AND C IN THE THREE-CHARACTER SHEET IDENTIFIERS ARE USED TO DENOTE THE APPROPRIATE DOMAIN. ASSIGNMENT OF RESIDUES TO SHEETS HAS BEEN DONE ON THE BASIS OF THE MAIN-CHAIN DIHEDRAL ANGLES (+- 25 DEGREES). RELATED HYDROGEN BONDS MAY DEVIATE SIGNIFICANTLY FROM ACCEPTED VALUES.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5578
Polymers71,8462
Non-polymers1,7116
Water00
1
R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules

R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,11416
Polymers143,6924
Non-polymers3,42212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18270 Å2
ΔGint-241 kcal/mol
Surface area47260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.400, 97.900, 81.600
Angle α, β, γ (deg.)90.00, 114.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.00212, -0.00057), (-0.00212, -1, -0.00125), (-0.00057, -0.00125, 1)
Vector: 0.00358, -0.01515, 0.05394)
DetailsTHE NON-CRYSTALLOGRAPHIC DIAD RELATING THE TWO SUBUNITS IS GIVEN ON THE MTRIX RECORDS BELOW. APPLYING THIS TRANSFORMATION TO THE RED SUBUNIT WILL YIELD APPROXIMATE COORDINATES FOR THE GREEN SUBUNIT. THIS DIAD CORRESPONDS CLOSELY TO THE CRYSTAL C-AXIS. THE TRANSFORMATION WAS DERIVED USING THE SYMMETRY AVERAGING PROCEDURE CONTAINED IN THE HENDRICKSON AND KONNERT PROGRAM. THIS CORRESPONDS TO THE R-AXIS OF THE P, Q, R SCHEME USED IN STRUCTURAL STUDIES OF OTHER SPECIES OF THE ENZYME.

-
Components

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


Mass: 35922.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
References: UniProt: P00354, UniProt: P04406*PLUS, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Compound detailsTURNS ARE SPECIFIED WHERE CA(N) TO CA(N+3) IS LESS THAN 5.7 ANGSTROMS AND O(N) TO N(N+3) IS LESS ...TURNS ARE SPECIFIED WHERE CA(N) TO CA(N+3) IS LESS THAN 5.7 ANGSTROMS AND O(N) TO N(N+3) IS LESS THAN 3.2 ANGSTROMS. MORE EXACT TURN DEFINITION MUST AWAIT HIGHER RESOLUTION REFINEMENT.
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal grow
*PLUS
pH: 5.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMEDTA12
25 mM2-mercaptoethanol12
35 mMNAD+12
46 mg/mlprotein11

-
Processing

RefinementRfactor Rwork: 0.33 / Highest resolution: 3.5 Å
Details: THE RESOLUTION COULD BE EXTENDED TO ABOUT 1.5 ANGSTROMS USING SYNCHROTRON RADIATION.
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 108 0 5154
Refinement
*PLUS
Highest resolution: 3.5 Å / Rfactor obs: 0.33
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