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- PDB-6m61: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor h... -

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Basic information

Entry
Database: PDB / ID: 6m61
TitleGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / heptelidic acid / Complex / OXIDOREDUCTASE PROTEIN
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 / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / cytosol / cytoplasm
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
Chem-F4F / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82449538629 Å
AuthorsYan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y.
CitationJournal: Chem Sci / Year: 2020
Title: Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance
Authors: Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y.
History
DepositionMar 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,08526
Polymers144,9854
Non-polymers3,10022
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-237 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.358, 135.078, 146.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules OQPR

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Peptidyl-cysteine S-nitrosylase GAPDH


Mass: 36246.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups

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Non-polymers , 7 types, 1173 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-F4F / (5aS,6R,9S,9aS)-9-methyl-9-oxidanyl-1-oxidanylidene-6-propan-2-yl-3,5a,6,7,8,9a-hexahydro-2-benzoxepine-4-carboxylic acid


Mass: 282.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M zinc acetate dihydrate, 0.1 M Sodium acetate trihydrate, pH 4.6, 12% w/v polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 142957 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 19.228006632 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 25.5
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.866 / Num. unique obs: 142957 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 1.82449538629→43.0321686884 Å / SU ML: 0.217157103773 / Cross valid method: FREE R-VALUE / σ(F): 1.33786284913 / Phase error: 22.4024440202
RfactorNum. reflection% reflection
Rfree0.227886023248 7010 4.98138199596 %
Rwork0.191578926319 --
obs0.193381921753 140724 98.073706512 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.5209129398 Å2
Refinement stepCycle: LAST / Resolution: 1.82449538629→43.0321686884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 190 1151 11441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063142641662210486
X-RAY DIFFRACTIONf_angle_d0.87693232136414184
X-RAY DIFFRACTIONf_chiral_restr0.06109789243021603
X-RAY DIFFRACTIONf_plane_restr0.005547308026821809
X-RAY DIFFRACTIONf_dihedral_angle_d7.771938463356175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8245-1.84520.3313718748891700.2749987714983298X-RAY DIFFRACTION74.0234791889
1.8452-1.86690.3258851661472120.2645767699943893X-RAY DIFFRACTION87.1364890681
1.8669-1.88970.2769278793742040.2456998709574170X-RAY DIFFRACTION91.3343077887
1.8897-1.91360.266515190622320.238592270754224X-RAY DIFFRACTION95.3155080214
1.9136-1.93880.2605326693832550.2209034083134426X-RAY DIFFRACTION97.7652464495
1.9388-1.96540.2595119612882060.2246127921354474X-RAY DIFFRACTION99.4052676296
1.9654-1.99340.2810514643982330.2169417029264546X-RAY DIFFRACTION99.8328807186
1.9934-2.02320.2666791021512220.2167719708554483X-RAY DIFFRACTION99.8938428875
2.0232-2.05480.2551311974342560.2126725029944465X-RAY DIFFRACTION99.9788225328
2.0548-2.08850.262020402542280.2193992500664559X-RAY DIFFRACTION100
2.0885-2.12450.2781599751982500.2161207461424454X-RAY DIFFRACTION99.9787460149
2.1245-2.16310.2470343235242530.2035721975654517X-RAY DIFFRACTION100
2.1631-2.20470.2689986339452670.206989460764485X-RAY DIFFRACTION100
2.2047-2.24970.2381330308292560.2022087522084485X-RAY DIFFRACTION100
2.2497-2.29870.2474280925142490.1985777966224511X-RAY DIFFRACTION99.9789960092
2.2987-2.35210.2365729056162250.1949279729624536X-RAY DIFFRACTION100
2.3521-2.41090.2534078633582140.199463663554545X-RAY DIFFRACTION100
2.4109-2.47610.2374071140142290.1992020673444552X-RAY DIFFRACTION100
2.4761-2.5490.2439816306162330.1955833987914539X-RAY DIFFRACTION99.9790488163
2.549-2.63120.2506584682952420.1976280930324516X-RAY DIFFRACTION99.9579831933
2.6312-2.72530.2359389927932590.19283339964529X-RAY DIFFRACTION100
2.7253-2.83440.2292205735942380.2007261498184531X-RAY DIFFRACTION100
2.8344-2.96330.2212867442622400.1892432520874551X-RAY DIFFRACTION100
2.9633-3.11950.2268393701572240.1902632502144590X-RAY DIFFRACTION100
3.1195-3.31490.2024527232572290.1830621357934588X-RAY DIFFRACTION100
3.3149-3.57070.197947889562150.1751802463574626X-RAY DIFFRACTION100
3.5707-3.92990.1891087397412490.1712791149464572X-RAY DIFFRACTION100
3.9299-4.4980.1754686994892100.1489954903184671X-RAY DIFFRACTION99.9795165916
4.498-5.6650.1905852234142600.1572747014374644X-RAY DIFFRACTION99.735611145
5.665-43.030.2283965389462500.1989716769194734X-RAY DIFFRACTION97.3627661653

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