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- PDB-8vhb: Crystal Structure of Human IDH1 R132Q in complex with NADPH and A... -

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Basic information

Entry
Database: PDB / ID: 8vhb
TitleCrystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Chem-EE1 / Chem-NDP / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMealka, M. / Sohl, C.D. / Huxford, T.
Funding support United States, 2items
OrganizationGrant numberCountry
American Cancer SocietyRSG-19-075-01-TBE United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM137773 United States
CitationJournal: Nat Commun / Year: 2024
Title: Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms.
Authors: Mealka, M. / Sierra, N.A. / Avellaneda Matteo, D. / Albekioni, E. / Khoury, R. / Mai, T. / Conley, B.M. / Coleman, N.J. / Sabo, K.A. / Komives, E.A. / Bobkov, A.A. / Cooksy, A.L. / Silletti, ...Authors: Mealka, M. / Sierra, N.A. / Avellaneda Matteo, D. / Albekioni, E. / Khoury, R. / Mai, T. / Conley, B.M. / Coleman, N.J. / Sabo, K.A. / Komives, E.A. / Bobkov, A.A. / Cooksy, A.L. / Silletti, S. / Schiffer, J.M. / Huxford, T. / Sohl, C.D.
History
DepositionDec 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,57942
Polymers194,0004
Non-polymers5,57838
Water19,2941071
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,97424
Polymers97,0002
Non-polymers2,97322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-128 kcal/mol
Surface area32790 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,60518
Polymers97,0002
Non-polymers2,60516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-103 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.404, 105.807, 109.782
Angle α, β, γ (deg.)90.000, 98.440, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / IDH1 / Cytosolic NADP-isocitrate dehydrogenase / IDPc / NADP(+)-specific ICDH / ...IDH / IDH1 / Cytosolic NADP-isocitrate dehydrogenase / IDPc / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 48500.117 Da / Num. of mol.: 4 / Mutation: R132Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Production host: Escherichia coli (E. coli)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)

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Non-polymers , 9 types, 1109 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CNS
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-EE1 / (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid / NADPH with ketoglutarate adduct


Mass: 889.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H34N7O22P3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1071 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 200mM NaSCN and 21%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.89→39.63 Å / Num. obs: 148142 / % possible obs: 97.12 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.71
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 14617 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→39.63 Å / SU ML: 0.226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 7516 5.07 %
Rwork0.1673 140626 -
obs0.1693 148142 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.39 Å2
Refinement stepCycle: LAST / Resolution: 1.89→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13074 0 324 1071 14469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813797
X-RAY DIFFRACTIONf_angle_d0.911618628
X-RAY DIFFRACTIONf_chiral_restr0.05812000
X-RAY DIFFRACTIONf_plane_restr0.00642361
X-RAY DIFFRACTIONf_dihedral_angle_d8.92361859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.36592480.30284467X-RAY DIFFRACTION93.24
1.91-1.930.30332540.26684699X-RAY DIFFRACTION97.06
1.93-1.960.3182470.23994686X-RAY DIFFRACTION97.28
1.96-1.980.29392310.22394655X-RAY DIFFRACTION97.45
1.98-2.010.24872520.21644680X-RAY DIFFRACTION96.65
2.01-2.030.25562730.20234613X-RAY DIFFRACTION96.5
2.03-2.060.23832230.20284405X-RAY DIFFRACTION91.16
2.06-2.090.24742300.19614660X-RAY DIFFRACTION96.93
2.09-2.130.24542460.19084710X-RAY DIFFRACTION97.77
2.13-2.160.23842370.19444755X-RAY DIFFRACTION98.02
2.16-2.20.23412380.19714706X-RAY DIFFRACTION97.92
2.2-2.240.25712440.19494767X-RAY DIFFRACTION98.25
2.24-2.280.23152460.17714718X-RAY DIFFRACTION97.52
2.28-2.330.22312600.17644681X-RAY DIFFRACTION97.71
2.33-2.380.23122840.18234687X-RAY DIFFRACTION97.84
2.38-2.440.25252630.18074676X-RAY DIFFRACTION97.44
2.44-2.50.23641880.18224547X-RAY DIFFRACTION92.82
2.5-2.560.23952610.18264675X-RAY DIFFRACTION96.82
2.56-2.640.22792410.18084765X-RAY DIFFRACTION98.6
2.64-2.720.21592450.17914754X-RAY DIFFRACTION98.23
2.72-2.820.24492630.18384734X-RAY DIFFRACTION98.12
2.82-2.930.23262560.18174741X-RAY DIFFRACTION98.4
2.93-3.070.20832930.17064708X-RAY DIFFRACTION98.44
3.07-3.230.20012320.16824630X-RAY DIFFRACTION95.05
3.23-3.430.21792420.16254700X-RAY DIFFRACTION96.98
3.43-3.70.19912540.1534811X-RAY DIFFRACTION99.2
3.7-4.070.15452530.14024814X-RAY DIFFRACTION98.79
4.07-4.660.15152640.124737X-RAY DIFFRACTION97.73
4.66-5.860.16552820.14244669X-RAY DIFFRACTION96.14
5.86-39.630.16952660.15194776X-RAY DIFFRACTION96.63
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.132615854320.01180064420181.400093138821.910060488640.08050467265734.87661841993-0.05017634011190.1693265350970.0076525419442-0.270378302832-0.0227369077304-0.561512926697-0.1803565679310.3278718606060.08923414229540.233820327694-0.01269690857410.1074957491060.22179925340.01774595554850.49470519563539.073-18.3756.556
20.9774831107920.04421286790010.221062104050.650860932335-0.1035653704151.55438037981-0.0371597247956-0.0850464681308-0.078884690143-0.08561693776990.0599753257543-0.08063303608950.1149788653540.0461870279154-0.02722790603720.176857666105-0.0006296914881330.01003498240130.117289033442-0.01218389683810.19894712425213.631-29.3938.988
32.18945881534-0.56308565926-0.04904104431792.796341443160.6292517329221.85333202626-0.0336308775085-0.2587778968970.08703259404660.120872299778-0.0313055833131-0.451949295741-0.0946398688510.1180388136860.07498496662140.170644568551-0.00812725564872-0.06765764736270.238318093895-0.003241029780540.36676918951534.236-14.26522.32
41.782020767910.173611534923-0.2916482561461.02459512018-0.1122109274781.50897091345-0.04446472741340.114603855691-0.161438756349-0.1788776665460.06202381392120.1521296493260.263314637165-0.142649764692-0.02970374513710.252912994316-0.0129701085063-0.03965380195730.123864258768-0.003810765123210.233631763509-15.051-18.8078.953
51.0723809846-0.118951519071-0.5469666148611.27715479550.2965118429831.615815338270.004475672941210.06907221450160.121061080903-0.1959829351050.0823642453339-0.10722782688-0.137881961216-0.0121190899616-0.08059841830470.202894277064-0.03141614322730.007804185866030.1203976086550.002430173338650.1989538567738.562-13.551-1.643
61.489633747020.00876538785179-0.003842335786730.978069243028-0.3582900428732.78661259570.0336704135479-0.1300594366540.01453612334510.07316557349990.04651422576980.151750806788-0.0595291169081-0.084807769932-0.07299797355480.144633981974-0.0113429196764-0.0009711681353670.111398533602-0.001788373289270.207915216608-14.866-12.58921.071
72.60945844956-0.06387039468752.348089711560.0230921612723-0.0375211548281.935774786790.008428278951990.378718571394-0.0292331297869-0.150812999995-0.1911889633160.163499686251-0.0431122003783-0.1686695395860.1577857019550.29625693038-0.0211566116297-0.05807184031950.9616301665810.01176983827540.33855304931-14.916-1.582-51.651
81.4934445099-0.3133795470961.679960849352.221429744290.1210070833842.261989224050.0287176891980.653482857219-0.2134191023370.2583885687340.04379797660250.1352147177220.350732194763-0.60168256001-0.1203377972580.240793075935-0.1607352776560.01594298691980.699306055018-0.02398210235470.28270724427-2.551-9.348-35.648
91.249003900840.363003327503-0.8584094658120.2778130918620.04778487588921.363313622060.03343605937561.064741622680.164897237909-0.1381725714390.1575933354520.211937100687-0.0111749233165-0.584439943003-0.114446809560.291772254138-0.0575516670296-0.0185048785220.8796716171750.08322235403870.24956645869612.776-3.94-50.499
101.294586357060.222388665812-0.6545794951650.6238707149860.127326551680.919296958951-0.2220356464490.614455270281-0.288266246645-0.1741598094790.1152117774780.01694120923620.351949335225-0.3033742228790.03669108322380.334501153605-0.1214709907220.03443598579070.441079551992-0.1338570757470.23470554869623.445-17.243-45.26
111.21082833197-0.584995502549-0.6370026809590.9974784980220.2964035165530.545207992090.2816582873071.552854584040.505305662886-0.0757036198389-0.2817001230970.0924431646901-0.084404166872-0.7829783893560.07372882363690.2558198112080.06401545486-0.07760337167151.232304327070.3017975535260.3243105446220.3123.761-49.565
124.280303219191.15768740736-0.2999175254621.97417982419-0.7070927567942.84611098169-0.115513054542-0.144781181088-0.2470453678010.0568296579063-0.00873276238992-0.4494686805020.2199522987440.9115525553920.09363769846840.2588007744440.09918337177730.006725734826860.639741156476-0.01396523142730.33019841642157.854-2.814-40.054
133.25540047382-0.148919724536-0.5670680236720.96858330321-0.2455626265682.52371346519-0.1201532728780.423003593317-0.191418930473-0.186006588349-0.00351050846479-0.1760600743470.4082645993260.249840712620.07670804752090.27709020187-0.005462105028330.02617897307410.270836599763-0.03359180027790.20530180772741.014-4.67-42.643
142.032781114870.57587709954-0.4144542273973.273662099940.07131841296811.22322300387-0.0520699504270.0493652242124-0.007520595887830.12721267904-0.004675397827830.03271153212040.120513603117-0.04566135613250.03136701795240.162384468893-0.007223909120940.006889511645810.152473021197-0.03310155088120.1199171229925.629-6.956-27.604
152.048910351490.374138924033-1.002421504531.12323391513-0.3663374867111.769995512910.009258348719690.3349294989050.1482910491-0.09864767596020.0276274489542-0.0999709819209-0.1796045309240.33086347884-0.03695224386650.209574960329-0.0404417585546-0.007562915778950.379937763760.01753353669310.22587701107943.9815.139-46.789
165.210534126611.60353064189-0.8149505375945.95725296356-0.8755452264935.72997014886-0.0262623992340.765367672752-0.135815640305-0.2805930721150.39845597192-0.506942670204-0.08267476956040.804743516458-0.3773517890250.227904695823-0.0323685640962-0.05536821489260.5779030809070.01946368685690.29208915655451.8818.38-52.022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:94 )A2 - 94
2X-RAY DIFFRACTION2( CHAIN A AND RESID 95:285 )A95 - 285
3X-RAY DIFFRACTION3( CHAIN A AND RESID 286:411 )A286 - 411
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:133 )B2 - 133
5X-RAY DIFFRACTION5( CHAIN B AND RESID 134:284 )B134 - 284
6X-RAY DIFFRACTION6( CHAIN B AND RESID 285:413 )B285 - 413
7X-RAY DIFFRACTION7( CHAIN C AND RESID -9:29 )C-9 - 29
8X-RAY DIFFRACTION8( CHAIN C AND RESID 30:94 )C30 - 94
9X-RAY DIFFRACTION9( CHAIN C AND RESID 95:133 )C95 - 133
10X-RAY DIFFRACTION10( CHAIN C AND RESID 134:284 )C134 - 284
11X-RAY DIFFRACTION11( CHAIN C AND RESID 285:409 )C285 - 409
12X-RAY DIFFRACTION12( CHAIN D AND RESID 0:67 )D0 - 67
13X-RAY DIFFRACTION13( CHAIN D AND RESID 68:133 )D68 - 133
14X-RAY DIFFRACTION14( CHAIN D AND RESID 134:260 )D134 - 260
15X-RAY DIFFRACTION15( CHAIN D AND RESID 261:393 )D261 - 393
16X-RAY DIFFRACTION16( CHAIN D AND RESID 394:412 )D394 - 412

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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