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- PDB-9rzz: PYCR1 in complex with pyrrolidine-1-sulfonic acid. -

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Basic information

Entry
Database: PDB / ID: 9rzz
TitlePYCR1 in complex with pyrrolidine-1-sulfonic acid.
ComponentsIsoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE / delta-1-pyrroline-5-carboxylate reductase / PYCR1 / cancer / crystallographic fragment screening (XFS) / molecular docking / inhibitors / proline metabolism
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / : / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
: / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRagin-Oh, W. / Ruszkowski, M. / Czerwonka, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2021/43/B/NZ7/01611 Poland
CitationJournal: Bioorg.Chem. / Year: 2025
Title: Crystallographic fragment screening reveals new starting points for PYCR1 inhibitor design.
Authors: Ragin-Oh, W. / Czerwonka, D. / Tran, L.H. / Forlani, G. / Ruszkowski, M.
History
DepositionJul 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,18320
Polymers179,8075
Non-polymers1,37715
Water14,556808
1
A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,36740
Polymers359,61410
Non-polymers2,75330
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)164.549, 88.040, 116.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-640-

HOH

21E-510-

HOH

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Components

#1: Protein
Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1


Mass: 35961.352 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-A1JKN / pyrrolidine-1-sulfonic acid


Mass: 151.184 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: Based on Morpheus 2.34 condition (Molecular Dimension), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M ...Details: Based on Morpheus 2.34 condition (Molecular Dimension), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M sodium oxamate, 0.1 M Tris (base), BICINE pH 8.5, 20% ethylene glycol, 10% PEG 8000, and supplemented with 10% ethylene glycol for cryoprotection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 1.7→46.55 Å / Num. obs: 185960 / % possible obs: 99.7 % / Redundancy: 13.77 % / Biso Wilson estimate: 24.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.12 / Net I/σ(I): 18.19
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 13.2 % / Rmerge(I) obs: 2.71 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 29800 / CC1/2: 0.456 / Rrim(I) all: 2.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.55 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 1857 1 %
Rwork0.1907 183990 -
obs0.1909 185847 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10114 0 85 808 11007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006510520
X-RAY DIFFRACTIONf_angle_d0.828414266
X-RAY DIFFRACTIONf_chiral_restr0.05011703
X-RAY DIFFRACTIONf_plane_restr0.00731838
X-RAY DIFFRACTIONf_dihedral_angle_d12.65823882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.39931410.399813963X-RAY DIFFRACTION99.42
1.74-1.80.39911420.355114065X-RAY DIFFRACTION99.92
1.8-1.850.31471420.327814045X-RAY DIFFRACTION99.87
1.85-1.920.28391420.279814042X-RAY DIFFRACTION99.75
1.92-20.26251410.248814043X-RAY DIFFRACTION99.64
2-2.090.24241420.21514050X-RAY DIFFRACTION99.57
2.09-2.20.20421420.198914078X-RAY DIFFRACTION99.48
2.2-2.340.18131410.175214017X-RAY DIFFRACTION99.38
2.34-2.520.20451420.171714150X-RAY DIFFRACTION99.67
2.52-2.770.19031440.172414208X-RAY DIFFRACTION99.97
2.77-3.170.20341440.173714270X-RAY DIFFRACTION99.97
3.17-3.990.17481450.159314330X-RAY DIFFRACTION99.76
3.99-46.550.20761490.165714729X-RAY DIFFRACTION99.48
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)
11.5967871907-0.02374026687533.721886743265.48518772566-1.315675111779.09648135059-0.6209305968760.1612583090950.561072552655-1.791696747040.3424652605711.52746187853-1.01391330832-0.6273570998410.2023266811351.0008179317-0.0193388418639-0.351258015420.4732109665880.05570007211640.82418926488211.771465284726.584126839843.9677011024
20.936583499659-1.2725966159-0.1097237887764.440888138350.4215193875810.3209382131940.09017476697950.146292977922-0.362270296846-0.706079290027-0.05095889724950.1123618356620.1269473415440.00123694547694-0.03741115815640.387261936515-0.003436699750020.0375183610640.25997352283-0.0332631299840.38060671316516.064471343221.14780827455.7865118757
30.958091036854-0.1958927354450.1005056059631.77458211237-0.3666548462910.952429727250.006784781205050.0346724376048-0.122635588048-0.1972902169660.0263270113736-0.2334362469530.04516813345150.0874145556693-0.04426632142710.1525072379220.01011172560430.03483394534130.207275428197-0.01677112465430.25646957880915.723944637843.081555658470.0119564599
46.111316863640.5845805049314.399852617616.955891510530.4335128410197.84767391583-0.03580132841341.00878211081-0.221723991177-0.9617018434230.111628786251-0.9498067487070.02197706800631.35102553706-0.03676407988120.45678348872-0.02089428546950.1297894027910.423598608774-0.05972864036790.8446156240733.629362665567.013486203754.3725915772
57.777758374221.572904835570.9424217002431.963002382281.692350295966.06067138827-0.2905240390.177736647926-0.175614369661-0.2950515961860.220266586373-1.022130302640.2441157955380.4523493663840.1280222026810.2492792462220.04786224668910.1308346924510.2970618651480.04637452958980.66608459393135.985786440960.659301609559.4011643562
63.42795890735-4.51568399689-0.9618043107398.74436991461-1.140378905022.586604369470.0636097718872-2.283410267370.3865409167882.754263009530.668827100007-1.776480058050.6207172731630.812019027105-0.6313334385851.01442925789-0.00651951641956-0.1965840347990.903276602593-0.05513146137680.77303252050440.95742895560.871215469571.5997968005
73.41000617706-1.037967926390.05612921452292.339045026610.831587473232.3171371553-0.0574244348556-0.1929474368650.2903971538410.1200705222870.111214519085-0.708461826979-0.0794300743390.318374089594-0.04894840870930.299134346035-0.0179413016070.02097294093760.313980822970.02233242427020.71728361750332.4477147273.4268933665.1805387324
82.299250822881.166480852990.07380218065147.53284106747-0.4643285133821.35567004231-0.07134906228160.09074415101520.523798956738-0.2654358833950.0494933994023-0.0162797946655-0.2214500602730.03038171477930.02211857908020.24968377956-0.005212880878610.06061707174280.2239320469250.04242212755790.3983240964822.799053248571.165821787559.6772245862
97.279120280620.8606909246081.460184287646.21749191234-2.096523949234.275560947330.01007868698790.5846521510350.146256469548-0.9984831094430.0835161113439-0.220080964258-0.1032673331980.113206043389-0.03736436489740.350034159507-0.0186007578070.1184991562440.2297124373540.03080861068870.32734389102221.915900427563.917851943552.5234656465
100.633035472626-0.387950906890.0971787644523.32505459455-1.351128879591.23905490708-0.02620656159520.04973343564010.0905854201024-0.209708396716-0.0133598917919-0.2753811877720.0547493180640.03604128072830.06164793465160.159413063269-0.006087479666070.05763462946990.212711601868-0.01324764763790.25292332193118.48444738143.976239046867.2311911214
113.733507330410.559787100875-0.1979565971595.809796740350.1042433146720.693448097045-0.06719813239620.4256293530730.15668622247-0.4856722930870.0784461219053-0.1348106071140.105742247894-0.0732471554909-0.004002095982630.1501829074530.006738319355930.004014751107260.2246677808440.02265481650480.2026128722393.7235061800936.668289138463.327386751
123.64678704236-0.557992688936-0.2580568967852.940169676180.4827413496145.0724282548-0.00636295229128-0.05225604635450.8282096091340.0836941861018-0.112205187612-0.113706083985-0.7060943760880.151991858530.0273567568910.2088020709750.0151571259079-0.02753182950380.21971388970.0119968137430.34296605515210.708394628961.623382594773.2249069021
136.537378554543.85736141212.276320808125.753179202482.343911397822.24908346360.1801219882280.2492476752460.941105699506-0.598669299901-0.0643646633214-0.663509056193-0.3721812573590.422304613372-0.2604361238810.4448524398370.006883782047170.1515950881210.3669855929830.01975131702150.79037772181742.897502967526.978990910188.8675806367
144.823389306723.54254619735-0.2787895138134.871268967661.869920048024.93631193188-0.4619446715570.7997353767150.9964223745-2.746802713170.329215444986-0.655771135372-1.330870860670.2552717079360.1493951111151.2433583086-0.01449953148030.12657063570.4869535996940.006622036732561.104081670246.741775174626.721833647782.1074418666
153.399584462921.21911818584-2.151301891997.50509996216-0.9811506169316.95699893451-0.05883750898930.3837513478770.127829055447-1.339623661080.127346842617-0.6141531391940.3931908876390.254879701861-0.1029403317390.5299310910920.04253957568540.02607181374880.2648004116470.005199678171780.58365026516238.233451814513.442942838687.3008467444
161.850519575840.903808313016-0.3030069160593.0404181658-0.8812040781262.72774039497-0.0575153592984-0.06871045479460.1346922107040.2459586368760.0521077342294-0.4932412531360.2817507362810.160610307634-0.01284515263680.2305225722970.0394848282802-0.1131276684640.221625599637-0.01176845405410.46031164206136.746168325721.36827154299.3284296602
171.04925158689-0.7633075895510.1193687089212.34495035483-0.7148180698390.719069673251-0.0222778010449-0.0334123841684-0.0158327517590.0683075507682-0.018877305879-0.4032171898450.0172312536120.07138935968910.062512189010.1340462583010.00413400167389-0.05466600188670.197990770937-0.01780157352930.31706496483126.702005587244.224411730892.6155937646
182.02718487846-0.4485470545110.1056629566953.669145575690.5599483821392.02417978431-0.029715111038-0.112496267398-0.08565634708470.2282188217810.0657536365835-0.2549582152890.1457046187780.056165826642-0.0488652963080.09016141714720.000718448468937-0.02088963952460.1814243074370.0358931386470.20456860082317.083974475839.790389024198.7296135127
194.55750874318-3.352867102811.061515609935.474379943062.277057131978.752800844880.0728699637221-0.387951473369-0.2587514696510.9185875463060.113705352442-0.1920096678670.002849943290260.0148207799189-0.1440556689790.435614725377-0.0794598431472-0.1451439127010.249640994230.08310159940580.44677361820136.098519108364.5267746669115.580041259
200.5259524979250.7710937075810.2064572181422.063232176760.2865334460610.575917748478-0.0136767529824-0.001453617497340.06618827377570.103618240636-0.003787779853-0.259916351399-0.1944630478770.08747662205540.01393756239080.211065713818-0.00121026806299-0.0763371440720.2155439586440.01013921720090.3850238532829.532744640957.893856050398.398534878
214.56059639443-0.456189052573-0.1538831702494.0671093756-0.4388254262944.003273587740.0832935718923-0.1529551757510.7037239370250.0743937478696-0.1234526817980.0539139831882-0.79480494304-0.005407420512980.04628010420060.251549001687-0.00600832756548-0.01245152278480.2134986451030.01994733962930.28773751569216.782358964862.147567128393.4716312257
226.74335876853-4.53603378042-2.428760477735.361617222833.151884632667.796741473820.0142998903228-0.3604617859980.278097233370.8223914190820.117510900231-1.17616330227-0.1568918898330.551298139573-0.09525281674120.608659139733-0.0452503336375-0.2678634506670.3823681856360.00729771182770.6380739121211.689087594726.9813134418128.780642102
233.82916460069-2.1742643192.915762005568.852504070853.378529066175.608650927680.154246774840.2318840305661.145747839650.1580832270950.189476391897-2.91150793319-0.4426433813630.9834645649-0.2427970873970.823404114728-0.0286773697328-0.1936809681960.4750494568420.07658805454551.3266448376419.513912517226.3762049423129.753416597
242.058425182710.1201255238360.2938640718195.66291905731-0.2468475785271.559656713455.83814126724E-5-0.144828897344-0.5195490023870.616639769740.0186168672802-0.5064247481660.1881900810940.207297106855-0.03872832309190.530557959388-0.00542209902385-0.08365087833440.2682455982490.07122060595850.4297461495836.0213592859717.2299742103125.142155062
251.108040088390.812993261117-0.3987198436493.94188661461-0.9936670346321.189214085020.0405418699715-0.110702195162-0.1464946663770.480322433151-0.0502977226786-0.2160681331680.0161681696308-0.00301380311950.01364682315360.2403175157770.0243529068505-0.03789689313840.1789333042830.003541115459550.1584585891513.1883542942844.1466533613114.494867606
262.87722824418-0.2410618944781.730338363785.50455220396-0.5357750080443.5193430426-0.0126123944852-0.3058952551870.02961601755390.5904719105040.164404293120.212308619321-0.122932631503-0.41121472565-0.1351369136410.201517888310.02082420990730.01637660983350.1991904450960.0148618789380.245880492184-11.158967028651.3788632871108.874774454
272.80241005781-0.6876394851230.1618046663455.49761339714-0.7512449006184.587297910770.1081512265980.140386615991-0.789629545329-0.00688628463646-0.178197268713-0.06717590701270.6072366944870.107144410567-0.06367566469450.18613218695-0.02153047063920.00384721591070.175723704075-0.0004307283887840.3250947592760.63089259486826.718051102105.224698837
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 48 )AA1 - 481 - 48
22chain 'A' and (resid 49 through 194 )AA49 - 19449 - 194
33chain 'A' and (resid 195 through 273 )AA195 - 273195 - 273
44chain 'B' and (resid -4 through 9 )BE-4 - 91 - 14
55chain 'B' and (resid 10 through 33 )BE10 - 3315 - 38
66chain 'B' and (resid 34 through 47 )BE34 - 4739 - 52
77chain 'B' and (resid 48 through 100 )BE48 - 10053 - 105
88chain 'B' and (resid 101 through 144 )BE101 - 144106 - 149
99chain 'B' and (resid 145 through 163 )BE145 - 163150 - 168
1010chain 'B' and (resid 164 through 219 )BE164 - 219169 - 224
1111chain 'B' and (resid 220 through 249 )BE220 - 249225 - 254
1212chain 'B' and (resid 250 through 273 )BE250 - 273255 - 278
1313chain 'C' and (resid 1 through 22 )CJ1 - 221 - 22
1414chain 'C' and (resid 23 through 48 )CJ23 - 4823 - 48
1515chain 'C' and (resid 49 through 110 )CJ49 - 11049 - 110
1616chain 'C' and (resid 111 through 163 )CJ111 - 163111 - 163
1717chain 'C' and (resid 164 through 219 )CJ164 - 219164 - 219
1818chain 'C' and (resid 220 through 273 )CJ220 - 273220 - 273
1919chain 'D' and (resid -3 through 62 )DN-3 - 621 - 66
2020chain 'D' and (resid 63 through 249 )DN63 - 24967 - 253
2121chain 'D' and (resid 250 through 273 )DN250 - 273254 - 277
2222chain 'E' and (resid 1 through 22 )EQ1 - 221 - 22
2323chain 'E' and (resid 23 through 48 )EQ23 - 4823 - 48
2424chain 'E' and (resid 49 through 163 )EQ49 - 16349 - 163
2525chain 'E' and (resid 164 through 219 )EQ164 - 219164 - 219
2626chain 'E' and (resid 220 through 249 )EQ220 - 249220 - 249
2727chain 'E' and (resid 250 through 273 )EQ250 - 273250 - 273

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