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- PDB-9p0u: Structure of PYCR1 complexed with the allosteric inhibitor 7-benz... -

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Basic information

Entry
Database: PDB / ID: 9p0u
TitleStructure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / AMINO-ACID BIOSYNTHESIS / OXIDOREDUCTASE / PROLINE BIOSYNTHESIS / INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Biochem.J. / Year: 2026
Title: Serendipitous Discovery of an Allosteric Inhibitor Binding Groove in the Proline Biosynthetic Enzyme Pyrroline-5-Carboxylate Reductase 1 (PYCR1).
Authors: Meeks, K.R. / Mattingly, C.J. / Nix, J.C. / Chuk, O. / Protopopov, M.V. / Tarkhanova, O.O. / Tanner, J.J.
History
DepositionJun 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)168,95515
Polymers167,6635
Non-polymers1,29210
Water13,241735
1
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)337,91030
Polymers335,32610
Non-polymers2,58420
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area61690 Å2
ΔGint-639 kcal/mol
Surface area87940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.602, 179.591, 88.199
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21A-490-

HOH

31E-411-

HOH

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 33532.574 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 (E. coli)
References: UniProt: P32322, pyrroline-5-carboxylate reductase

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Non-polymers , 5 types, 745 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-A1CFH / 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid


Mass: 343.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Resevoir contained 400 mM Li2SO4, 13% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 12 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid. Crystal was soaked in ...Details: Resevoir contained 400 mM Li2SO4, 13% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 12 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 100 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.66→90.7 Å / Num. obs: 374809 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Χ2: 1.05 / Net I/σ(I): 12
Reflection shellResolution: 1.66→1.69 Å / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.303 / Num. measured all: 64205 / Num. unique obs: 9400 / CC1/2: 0.55 / Rpim(I) all: 0.53 / Rrim(I) all: 1.409 / Χ2: 0.83 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.66→61.56 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 19156 5.11 %
Rwork0.1832 --
obs0.1843 374809 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→61.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9706 0 80 735 10521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610030
X-RAY DIFFRACTIONf_angle_d0.82213681
X-RAY DIFFRACTIONf_dihedral_angle_d11.9483463
X-RAY DIFFRACTIONf_chiral_restr0.0511680
X-RAY DIFFRACTIONf_plane_restr0.0081772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.33486600.305311809X-RAY DIFFRACTION98
1.68-1.70.33816530.299511910X-RAY DIFFRACTION98
1.7-1.720.32926030.310911818X-RAY DIFFRACTION98
1.72-1.740.31936110.304111784X-RAY DIFFRACTION98
1.74-1.760.31576520.292511571X-RAY DIFFRACTION96
1.76-1.790.29476760.272311631X-RAY DIFFRACTION96
1.79-1.810.27816270.264111930X-RAY DIFFRACTION99
1.81-1.840.25246960.243211898X-RAY DIFFRACTION99
1.84-1.870.23856900.234411889X-RAY DIFFRACTION99
1.87-1.90.24866680.233211879X-RAY DIFFRACTION99
1.9-1.930.25515890.236911966X-RAY DIFFRACTION98
1.93-1.970.25446290.230411942X-RAY DIFFRACTION99
1.97-2.010.22955710.222412002X-RAY DIFFRACTION99
2.01-2.050.2256470.211911993X-RAY DIFFRACTION99
2.05-2.090.22026280.20911728X-RAY DIFFRACTION98
2.09-2.140.24196340.197111910X-RAY DIFFRACTION99
2.14-2.190.22076270.189611952X-RAY DIFFRACTION99
2.19-2.250.21595990.189111818X-RAY DIFFRACTION98
2.25-2.320.20266380.181611807X-RAY DIFFRACTION98
2.32-2.390.19915860.169711957X-RAY DIFFRACTION98
2.39-2.480.1727050.167511466X-RAY DIFFRACTION96
2.48-2.580.17336300.158511767X-RAY DIFFRACTION98
2.58-2.70.17546540.162312010X-RAY DIFFRACTION99
2.7-2.840.20036080.170611999X-RAY DIFFRACTION99
2.84-3.020.20066400.176611949X-RAY DIFFRACTION99
3.02-3.250.20616730.17211874X-RAY DIFFRACTION99
3.25-3.580.17825710.168111917X-RAY DIFFRACTION99
3.58-4.090.17416770.151111891X-RAY DIFFRACTION99
4.09-5.160.16266750.141711650X-RAY DIFFRACTION97
5.16-61.560.18916390.173611936X-RAY DIFFRACTION99
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)
10.70490.08370.83230.2911-0.03522.63320.0722-0.2089-0.01580.1143-0.0266-0.05310.11010.0969-0.03230.1365-0.0009-0.03240.2262-0.00420.197426.3073173.873924.6099
21.30610.3846-0.99120.5206-0.12761.86330.04660.01650.0648-0.13850.0175-0.1051-0.21360.3535-0.0640.1716-0.0247-0.00970.2451-0.00530.208532.9369183.195-5.9657
30.3862-0.2018-0.03061.0591-0.16281.5952-0.1102-0.1705-0.14170.2722-0.00510.0840.50130.02060.08890.38880.04220.04730.18710.03380.22910.44139.807218.878
40.9074-0.5204-0.41250.98240.23451.66210.00860.1094-0.0768-0.1969-0.0758-0.20840.31390.44210.03950.2780.11010.03240.25670.02240.249225.7915144.7411-7.8347
50.83320.2196-0.48211.13760.16071.48690.172-0.30410.17110.3037-0.11530.0513-0.3020.1347-0.0340.2295-0.05150.00490.197-0.03720.2117-0.0303200.93615.7962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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