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- PDB-27fm: Crystal structure of human glyceraldehyde-3-phosphate dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 27fm
TitleCrystal structure of human glyceraldehyde-3-phosphate dehydrogenase bound to gold(I)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / gold(I) / active site / glycolysis
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) / : / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / canonical glycolysis ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / : / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / canonical glycolysis / negative regulation of formation of translation preinitiation complex / GAIT complex / peptidyl-cysteine S-nitrosylase activity / defense response to fungus / regulation of macroautophagy / positive regulation of type I interferon production / lipid droplet / glycolytic process / positive regulation of cytokine production / cellular response to type II interferon / microtubule cytoskeleton organization / NAD binding / disordered domain specific binding / NADP binding / neuron apoptotic process / microtubule cytoskeleton / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / microtubule binding / vesicle / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / protein stabilization / ribonucleoprotein complex / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / nucleus / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / : / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsHaibo, W. / Xinhua, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of human glyceraldehyde-3-phosphate dehydrogenase bound to gold(I)
Authors: Haibo, W. / Xinhua, X.
History
DepositionMay 28, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,30310
Polymers144,3974
Non-polymers9066
Water23,8161322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-111 kcal/mol
Surface area44640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.880, 128.590, 81.750
Angle α, β, γ (deg.)90.000, 117.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 36099.168 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 (E. coli)
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M D,L-malic acid, 20% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.46→64.3 Å / Num. obs: 254607 / % possible obs: 99.85 % / Redundancy: 12 % / Biso Wilson estimate: 15.06 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.07
Reflection shellResolution: 1.46→1.48 Å / Rmerge(I) obs: 0.854 / Num. unique obs: 8464

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→64.3 Å / SU ML: 0.119 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1667 12411 4.87 %
Rwork0.1507 242196 -
obs0.1515 254607 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 1.46→64.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10035 0 12 1322 11369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005110241
X-RAY DIFFRACTIONf_angle_d0.827213880
X-RAY DIFFRACTIONf_chiral_restr0.08211580
X-RAY DIFFRACTIONf_plane_restr0.0051801
X-RAY DIFFRACTIONf_dihedral_angle_d7.811408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.25874330.23988033X-RAY DIFFRACTION99.86
1.48-1.490.24844210.2288039X-RAY DIFFRACTION99.83
1.49-1.510.23543730.21628042X-RAY DIFFRACTION99.86
1.51-1.530.22333200.21038164X-RAY DIFFRACTION99.89
1.53-1.550.20723750.19818136X-RAY DIFFRACTION99.91
1.55-1.570.20014030.19368034X-RAY DIFFRACTION99.96
1.57-1.60.2114290.18637989X-RAY DIFFRACTION99.95
1.6-1.620.19994060.19138113X-RAY DIFFRACTION99.89
1.62-1.640.20323870.17948076X-RAY DIFFRACTION99.94
1.64-1.670.18584270.16988028X-RAY DIFFRACTION99.99
1.67-1.70.16764090.16518065X-RAY DIFFRACTION99.95
1.7-1.730.20554210.16228068X-RAY DIFFRACTION99.99
1.73-1.760.1724710.15738007X-RAY DIFFRACTION99.96
1.76-1.80.16013870.15268040X-RAY DIFFRACTION99.98
1.8-1.840.1714340.15028089X-RAY DIFFRACTION100
1.84-1.880.17154310.14628057X-RAY DIFFRACTION99.99
1.88-1.930.15413910.14138077X-RAY DIFFRACTION100
1.93-1.980.16823770.14348121X-RAY DIFFRACTION99.99
1.98-2.040.17854370.14618064X-RAY DIFFRACTION99.98
2.04-2.110.15894520.13998031X-RAY DIFFRACTION99.98
2.11-2.180.15223740.13848100X-RAY DIFFRACTION99.99
2.18-2.270.15864270.14088109X-RAY DIFFRACTION99.95
2.27-2.370.15894980.14357951X-RAY DIFFRACTION99.86
2.37-2.50.16944130.14978090X-RAY DIFFRACTION100
2.5-2.650.16654710.15238006X-RAY DIFFRACTION99.98
2.65-2.860.16534040.15298125X-RAY DIFFRACTION99.98
2.86-3.150.16083920.14848130X-RAY DIFFRACTION99.81
3.15-3.60.1463820.13348108X-RAY DIFFRACTION99.86
3.6-4.540.13944220.1278137X-RAY DIFFRACTION99.92
4.54-64.30.16874440.15198167X-RAY DIFFRACTION99.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.01376329723-0.0570013938322-0.4416374009580.464306782878-0.2443272854641.39279262737-0.04369384389460.0409682672120.078335455173-0.07619650253860.01851111059630.1070353247960.0331651679687-0.1161315347840.0171207202470.1527605500410.013330473733-0.04284231960390.106095230384-0.003927253263270.1448398721940.27300147141334.35938216639.78543718574
20.5541374213630.441135431614-0.3737401550540.966928600959-0.2826536473110.430650145738-0.009510752087010.1045364194380.0549712290944-0.1354539474340.03841901210420.0291041691554-0.0410728398471-0.065266860393-0.028032849310.1434230992250.00927063595206-6.70203214269E-50.1471537380890.01118135882490.10847682401818.967783060519.018518048.15866458192
30.472494928198-0.113169491770.04357116102720.801569241244-0.06045739440360.597326219579-0.0331917973987-0.01125497761690.0517008271369-0.06370579995040.0122889639049-0.0906344242909-0.08061747236110.07327456699560.02013179251620.119055856277-0.01031570856070.005971693318950.117061760680.0053484141230.11055761702125.459920838929.360377497613.371198803
41.96101339762-0.373640067213-0.001512340597370.5448305942340.469064692871.750498537430.0738619551645-0.0152323846153-0.06618509055020.166632550794-0.0368177599879-0.07649960254490.0930658651124-0.107801361983-0.03070297426980.1511434205660.000874861346391-0.005200962248920.1185721677450.01564706798580.16772846915432.1458679356-10.224530975834.7759084291
52.2094873392-0.7858164692520.07378568478081.463796103920.09700834790932.11812175050.000651272291711-0.121132545646-0.1024647237040.19386458870.0398376880265-0.06977715439740.215284294786-0.0556731760195-0.01772849000160.198755548143-0.0247756090064-0.002246324658090.1216989741910.008690496601770.16093612338723.7579564114-7.9088423659342.2184722565
65.52727461982.726816263440.6928502986783.335369793570.2048664441992.092746429340.182371899305-0.4436894367690.06190717042350.384804990978-0.190393868824-0.162948401042-0.01389365679720.194334476955-0.0009796332880240.267258750220.00491941980461-0.05915491221640.168629087328-0.0008602757317650.18976571949137.9122330803-8.7700352490745.6910959867
70.7239568913890.00319459755608-0.1120112670410.963398529507-0.458979928091.833873263840.00694218805808-0.08145666969690.04556227864410.130010287925-0.093072843881-0.261268006746-0.03333150922810.190559656750.07008348046460.1307667778280.00838023672761-0.03945870655260.1348643096260.02060324467530.23641456857844.6320659807-4.5504507415132.8232248049
80.425820416411-0.09837397212940.3748962618110.717557113189-0.6769571698311.714084319580.03027976561980.0381852889015-0.0351935526409-0.0629006120132-0.0489340176047-0.2163393215680.05704428578320.1046187601560.03767296191170.1191299080670.01824691775110.01637717646450.1342760129740.01442224928680.20568202669541.4358465883-2.9742219983916.6371656472
90.495195744229-0.256304860097-0.5613833000630.7651956856490.5165335236430.840200055901-0.0162454967365-0.05316211243160.01668770952350.03360334995640.0429783285628-0.1260067489160.05040330175850.127627585772-0.03177178831680.1158310434950.011129065875-0.001831397310170.1525442240040.009392089142960.12976850360630.681617911914.852060008925.2180416522
101.18517785963-0.169804740977-0.6698165994591.129608352740.2598339847920.697247034269-0.00124848739929-0.09812271520890.01286295724120.02871641457310.0231346378125-0.1442207588770.02954503773410.143357249553-0.03714425685680.104024512760.016463013053-0.007953870978020.1596798508520.009628037184750.12195883824234.15300497289.7001715737517.585232266
110.966904497450.16888629796-0.9248926800641.50731169997-0.7856148025833.185466327270.001131816860620.173535486739-0.120256717422-0.309170440546-0.0189402715332-0.1288819433190.115110928685-0.09305596593920.01175758354190.1259524807790.01869532283590.03072889728230.149718412121-0.01628667232820.12306743275831.06349799472.569959119122.63389211179
121.24534703784-0.396828970346-0.009337208293111.529637315440.1062023704381.727388094730.0378955456360.227950019321-0.219691012694-0.124372894167-0.0945159867065-0.04001354125350.1503510972380.00917513368936-0.01042019275680.162268854916-0.003393912079690.01211724798620.142688916787-0.02779693923960.14901896548824.4615731261-4.521739136569.91011402122
130.379906340663-0.06909847659410.02872897496080.839005885956-0.2491135400940.8737094473360.007797648708820.0413395415517-0.0598841915788-0.0597131076708-0.00216348709585-0.07602464494410.0581929643611-0.00941210218150.008879886937380.09980749793570.002813510316410.01079684719390.102580881288-0.007861096830150.11476490172729.8461766588-1.33978728316.3467283147
141.11633529513-0.1112278931-0.324595347081.010180023530.7878162535921.734160898820.005546744365030.0336320360060.1420242785410.07051119835740.0197206726166-0.137614348332-0.06439600192340.057367078429-0.01951470435770.159833219868-0.00365908591488-0.02113027894020.1207631753230.009702301282580.16739292507124.840316432434.311598576641.9722562708
151.584809610360.44958648217-0.1356113619111.04500635504-0.3656371519921.236348011620.0806627233899-0.2580766188170.03381366841860.209927401667-0.105497387777-0.1455042072220.004083521269390.1163280532380.02684882274410.207711299978-0.0139678824535-0.04252801975830.152039810633-0.01534673290540.15006761228521.728963122231.178780689958.4238330571
160.668717302517-0.406102458388-0.7504350682710.5428473506620.3968538324570.849502021002-0.00175831924788-0.07820254276880.04506010937080.1004443706890.0344383401294-0.0127608478609-0.01974984845070.0461608012737-0.03489384186520.142659152228-0.002952820841580.004801856582390.148611188529-0.006582161166960.1176699124786.9059949011914.498002268749.7979407492
170.5995908294670.115785272794-0.05969777107620.7339942906740.02504418510540.665167763605-0.009122978522710.008414293993080.08171766735080.07873838302830.005356338497290.115101287812-0.0729813540227-0.08506929008780.005485740137990.1231383262590.01615121871950.01867750351910.124176753021-0.001602825965020.112010042333-1.1261121226924.535551900246.3307586257
181.78244363546-0.2389169818040.3087595423451.49910338926-0.5696835908142.251825517940.102386784524-0.0380328393787-0.037596909083-0.0864916952797-0.02029449424940.03224419790590.1381520581740.158141121958-0.06927598685850.0996531675781-0.00688047164411-0.004390480377260.109987174397-0.0291100952340.109262366339-2.78079908026-11.275691281818.4508800675
190.9620133619970.9092631409270.1401650124491.812057819561.378299607962.27452440355-0.02788019532420.146826162462-0.0988894231811-0.08272046694390.1080345331990.05693864070940.04250758514390.102330072837-0.1224719555970.143006211568-0.00110330207962-0.003955464478810.138501680366-0.03315348718150.1546102879585.31976081954-6.5510527908411.6101535743
206.31087875422-2.909781842860.1112534846413.280990095750.4367629530931.553267111810.2542619440180.3003411867230.0295226044095-0.258298765294-0.1600205500860.0750078701931-0.0684614410577-0.108894433997-0.09301725144890.213919848201-0.00507037543065-0.0338861444450.154386842963-0.0113645929890.15465480429-8.52935170353-8.443812975887.72530718752
210.3679329823070.0352055577716-0.1371612992810.6087781375670.169527101061.480312930450.02956159502740.037972904555-0.00463257404539-0.0436811270705-0.006855500224430.151524074632-0.0130582118432-0.100587796588-0.02133154996180.0965765061218-0.00726179969604-0.01204283029150.127889725843-0.008673490352850.182878568931-14.3692134344-7.7311381361327.7993793883
220.6608766354620.422711083715-0.6981965872611.22621822805-0.8000870778640.8759942565050.006228142112550.09653779633380.0160682082112-0.03629412766660.03806302748290.1386175228380.0299724546574-0.146268310863-0.05077138866470.117974111281-0.00409074651449-0.005426432321620.165222636377-0.008476298696780.127069631844-4.3830014683511.779097254332.1786406983
232.242166871230.404578671801-0.7433441583651.56245567275-0.1554796229210.636192616440.02712986331490.02397982589110.00733564219701-0.01472916887570.005691123169540.142591468570.0148150370976-0.104228596568-0.04332904826990.0965074274505-0.0128773828615-0.01503933695350.1553053000240.002374812905610.101530008726-6.997654215734.9623091621938.8273165388
241.1954367481-0.273246908393-0.7516464025121.605710525040.3151333137632.89798848754-0.00440138947533-0.156879215795-0.1336181908270.334448680893-0.05007691322140.1519388939250.1071342863970.06115568427410.0392700669750.145669882709-0.02923057935680.02457026801590.1590065911570.008953329604710.141204676637-2.82816656711-4.1676422525252.3262020499
250.3451892586140.1659034549180.3068853842730.64895101870.2342288048820.8494569285320.0253725670835-0.029272012552-0.07312959029280.0723498499641-0.01646313653140.04695643256990.032150396377-0.0103364373505-0.01540184937710.0894396846243-0.002438201187940.007780686772810.1028308055920.003275196382460.111370971398-0.038711814494-6.1049303773539.3512036943
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 151 )AA3 - 1511 - 149
22chain 'A' and (resid 152 through 227 )AA152 - 227150 - 225
33chain 'A' and (resid 228 through 335 )AA228 - 335226 - 333
44chain 'B' and (resid 3 through 34 )BC3 - 341 - 32
55chain 'B' and (resid 35 through 69 )BC35 - 6933 - 67
66chain 'B' and (resid 70 through 86 )BC70 - 8668 - 84
77chain 'B' and (resid 87 through 136 )BC87 - 13685 - 134
88chain 'B' and (resid 137 through 168 )BC137 - 168135 - 166
99chain 'B' and (resid 169 through 220 )BC169 - 220167 - 218
1010chain 'B' and (resid 221 through 240 )BC221 - 240219 - 238
1111chain 'B' and (resid 241 through 267 )BC241 - 267239 - 265
1212chain 'B' and (resid 268 through 282 )BC268 - 282266 - 280
1313chain 'B' and (resid 283 through 335 )BC283 - 335281 - 333
1414chain 'C' and (resid 3 through 69 )CF3 - 691 - 67
1515chain 'C' and (resid 70 through 151 )CF70 - 15168 - 149
1616chain 'C' and (resid 152 through 227 )CF152 - 227150 - 225
1717chain 'C' and (resid 228 through 335 )CF228 - 335226 - 333
1818chain 'D' and (resid 3 through 34 )DI3 - 341 - 32
1919chain 'D' and (resid 35 through 69 )DI35 - 6933 - 67
2020chain 'D' and (resid 70 through 86 )DI70 - 8668 - 84
2121chain 'D' and (resid 87 through 168 )DI87 - 16885 - 166
2222chain 'D' and (resid 169 through 220 )DI169 - 220167 - 218
2323chain 'D' and (resid 221 through 240 )DI221 - 240219 - 238
2424chain 'D' and (resid 241 through 267 )DI241 - 267239 - 265
2525chain 'D' and (resid 268 through 335 )DI268 - 335266 - 333

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