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- PDB-9p0v: Structure of PYCR1 complexed with the allosteric inhibitor 7-benz... -

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Basic information

Entry
Database: PDB / ID: 9p0v
TitleStructure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid in a remote site and NADH and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric 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 / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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)173,36820
Polymers167,6635
Non-polymers5,70515
Water16,195899
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)346,73540
Polymers335,32610
Non-polymers11,41030
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area71110 Å2
ΔGint-601 kcal/mol
Surface area86760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.757, 180.373, 88.206
Angle α, β, γ (deg.)90.00, 106.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

21A-529-

HOH

31E-417-

HOH

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Components

#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
#2: Chemical
ChemComp-G8I / (2S)-2-hydroxy-3,3-dimethylbutanoic acid


Mass: 132.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1CFH / 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid


Mass: 343.354 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Resevoir contained 340 mM Li2SO4, 12% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 20 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid, 3.5 mM NADH, and 10 mM (S)- ...Details: Resevoir contained 340 mM Li2SO4, 12% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 20 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid, 3.5 mM NADH, and 10 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid. Crystal was soaked in cryobuffer containing 20% PEG 200, 88 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid, and 15 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric 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: 1.8→92.14 Å / Num. obs: 302248 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Χ2: 1.04 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 97.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.14 / Num. measured all: 50097 / Num. unique obs: 7432 / CC1/2: 0.515 / Rpim(I) all: 0.882 / Rrim(I) all: 2.319 / Χ2: 1 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→42.04 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 15356 5.08 %
Rwork0.1733 --
obs0.1747 302248 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9871 0 385 899 11155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710617
X-RAY DIFFRACTIONf_angle_d0.86714519
X-RAY DIFFRACTIONf_dihedral_angle_d12.7123662
X-RAY DIFFRACTIONf_chiral_restr0.051740
X-RAY DIFFRACTIONf_plane_restr0.0081833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35145020.32429214X-RAY DIFFRACTION96
1.82-1.840.335120.30249553X-RAY DIFFRACTION98
1.84-1.860.31255440.27139444X-RAY DIFFRACTION98
1.86-1.890.28825060.26299558X-RAY DIFFRACTION98
1.89-1.910.30225200.26469305X-RAY DIFFRACTION97
1.91-1.940.31084540.25349351X-RAY DIFFRACTION96
1.94-1.970.2694870.23789352X-RAY DIFFRACTION96
1.97-20.26635180.23639628X-RAY DIFFRACTION99
2-2.030.22695050.2189637X-RAY DIFFRACTION100
2.03-2.060.23685430.19789607X-RAY DIFFRACTION100
2.06-2.10.23564530.19589691X-RAY DIFFRACTION100
2.1-2.130.22755010.18399707X-RAY DIFFRACTION100
2.13-2.180.21465680.18059615X-RAY DIFFRACTION100
2.18-2.220.17684670.17029675X-RAY DIFFRACTION100
2.22-2.270.23415440.18849634X-RAY DIFFRACTION99
2.27-2.320.19575370.16969666X-RAY DIFFRACTION100
2.32-2.380.21964480.17779680X-RAY DIFFRACTION100
2.38-2.440.22725440.17899594X-RAY DIFFRACTION100
2.44-2.510.20635180.16779654X-RAY DIFFRACTION100
2.51-2.60.19794550.16239744X-RAY DIFFRACTION100
2.6-2.690.17965700.16499557X-RAY DIFFRACTION100
2.69-2.80.21125550.16739613X-RAY DIFFRACTION100
2.8-2.920.21045180.1679601X-RAY DIFFRACTION99
2.92-3.080.20874920.16829610X-RAY DIFFRACTION99
3.08-3.270.1895520.16329615X-RAY DIFFRACTION99
3.27-3.520.19725000.16169421X-RAY DIFFRACTION97
3.52-3.880.16615060.14619234X-RAY DIFFRACTION96
3.88-4.440.15764730.13469683X-RAY DIFFRACTION100
4.44-5.590.15035210.14219698X-RAY DIFFRACTION100
5.59-42.040.17425430.16249551X-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)
10.52440.14850.25620.23840.0922.55190.0308-0.15640.00740.0857-0.0217-0.03890.00950.22520.00080.1181-0.0061-0.02320.1746-0.00950.183226.3632173.610824.3026
20.92980.1357-0.78740.3001-0.16661.72930.0495-0.05130.0552-0.0342-0.0217-0.0983-0.23690.3074-0.01450.1518-0.0348-0.02530.1636-0.01430.186533.3356183.1216-6.1154
30.4361-0.118-0.1460.6198-0.1691.478-0.0964-0.1312-0.13150.15560.00340.01790.35950.07380.08650.26750.04710.01930.13550.01970.206510.3846138.691719.3637
40.5901-0.2636-0.40020.68120.12441.7705-0.05060.0148-0.0565-0.1041-0.0075-0.14210.25910.44140.04820.19740.07050.00520.21410.01120.210626.5367144.582-8.3578
50.6666-0.0898-0.58150.94010.29091.47620.0658-0.2170.12150.1611-0.00410.0108-0.25680.1669-0.03760.1731-0.0217-0.01590.1504-0.01930.18860.0978201.04415.9293
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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