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- PDB-9q45: Quaternary complex of PYCR1 with the allosteric inhibitor 1-benzy... -

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Basic information

Entry
Database: PDB / ID: 9q45
TitleQuaternary complex of PYCR1 with the allosteric inhibitor 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid in a remote site and NADH and (S)-tetrahydrofuran-2-carboxylic acid in the active site
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
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 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
DepositionAug 19, 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

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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)172,36019
Polymers167,6635
Non-polymers4,69714
Water15,115839
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)344,71938
Polymers335,32610
Non-polymers9,39328
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area71280 Å2
ΔGint-605 kcal/mol
Surface area85120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.040, 179.738, 88.217
Angle α, β, γ (deg.)90.00, 106.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

21A-509-

HOH

31E-409-

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, 853 molecules

#2: Chemical
ChemComp-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1CFK / 1-benzyl-1H-1,3-benzimidazole-2-sulfonic acid


Mass: 288.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Resevoir contained 340-400 mM Li2SO4, 12-17% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 7 mM 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid, 3.5 mM NADH, and 10 mM L- ...Details: Resevoir contained 340-400 mM Li2SO4, 12-17% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 7 mM 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid, 3.5 mM NADH, and 10 mM L-tetrahydrofuroic acid. Crystal was soaked in cryobuffer containing 20% PEG 200, 44 mM 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid, and 15 mM L-tetrahydrofuroic 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: Feb 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→91.51 Å / Num. obs: 304360 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 8.6
Reflection shellResolution: 1.79→1.82 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7661 / CC1/2: 0.257

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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: 1.79→55.57 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 15515 5.1 %
Rwork0.1966 --
obs0.1981 304360 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9806 0 314 839 10959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610446
X-RAY DIFFRACTIONf_angle_d0.85114274
X-RAY DIFFRACTIONf_dihedral_angle_d13.3163923
X-RAY DIFFRACTIONf_chiral_restr0.0491732
X-RAY DIFFRACTIONf_plane_restr0.0081821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.40785650.36739492X-RAY DIFFRACTION99
1.81-1.830.37425250.35929633X-RAY DIFFRACTION99
1.83-1.850.38065150.33979664X-RAY DIFFRACTION98
1.85-1.880.35435300.33299569X-RAY DIFFRACTION98
1.88-1.90.38015090.33589369X-RAY DIFFRACTION98
1.9-1.930.37515130.35779578X-RAY DIFFRACTION97
1.93-1.960.33134670.3069379X-RAY DIFFRACTION96
1.96-1.980.32355100.29469569X-RAY DIFFRACTION99
1.98-2.020.30795180.28099666X-RAY DIFFRACTION99
2.02-2.050.28295220.25989658X-RAY DIFFRACTION99
2.05-2.080.29084850.25729782X-RAY DIFFRACTION99
2.08-2.120.29875080.2479591X-RAY DIFFRACTION100
2.12-2.160.2825480.24169650X-RAY DIFFRACTION99
2.16-2.210.25264890.23329798X-RAY DIFFRACTION99
2.21-2.260.32455430.27639527X-RAY DIFFRACTION98
2.26-2.310.24515270.23529666X-RAY DIFFRACTION99
2.31-2.370.24244670.19969682X-RAY DIFFRACTION99
2.37-2.430.25075450.19959659X-RAY DIFFRACTION99
2.43-2.50.21185010.18289713X-RAY DIFFRACTION100
2.5-2.580.19924680.17349720X-RAY DIFFRACTION99
2.58-2.670.19175770.17779631X-RAY DIFFRACTION99
2.67-2.780.22765570.17929651X-RAY DIFFRACTION99
2.78-2.910.21795050.17859632X-RAY DIFFRACTION100
2.91-3.060.21534990.17439711X-RAY DIFFRACTION99
3.06-3.250.20425450.16359691X-RAY DIFFRACTION99
3.25-3.50.18845130.1669580X-RAY DIFFRACTION98
3.5-3.860.19535160.15899404X-RAY DIFFRACTION97
3.86-4.410.15954790.13349790X-RAY DIFFRACTION100
4.41-5.560.1535200.14229732X-RAY DIFFRACTION100
5.56-55.570.1735490.15929658X-RAY DIFFRACTION100
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)
10.54090.09150.49790.3105-0.14012.310.0303-0.13540.02240.0927-0.0594-0.046-0.01250.12960.03430.117-0.0127-0.02310.1862-0.01250.193526.6038174.182224.3737
21.05540.2445-0.79370.4214-0.25651.80370.0455-0.0570.0286-0.0497-0.0342-0.1128-0.20380.3336-0.01030.1349-0.0204-0.02260.1854-0.01120.186432.9345183.4067-6.0521
30.5776-0.2259-0.24180.9214-0.20331.5839-0.1512-0.1548-0.17060.21520.01170.04640.42730.09760.09640.32140.06310.05050.15240.03330.234610.2822139.5318.9965
40.6599-0.1832-0.42160.929-0.14291.8763-0.1118-0.004-0.1151-0.163-0.0812-0.19160.36560.4690.12770.26240.10160.04410.21690.03910.253226.3144.9175-7.9966
50.7535-0.0754-0.64211.15980.29361.69710.0853-0.24110.15140.2141-0.0210.0408-0.30630.19-0.03270.1838-0.027-0.00470.1663-0.02070.20360.0832201.175415.7293
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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