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- PDB-3gpd: TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-... -

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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 / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex / peptidyl-cysteine S-nitrosylase activity / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / disordered domain specific binding / NADP binding / microtubule cytoskeleton / neuron apoptotic process / nuclear membrane / microtubule binding / vesicle / killing of cells of another organism / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / 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
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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