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- PDB-7klm: Human Arginase1 Complexed with Inhibitor Compound 24a -

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Basic information

Entry
Database: PDB / ID: 7klm
TitleHuman Arginase1 Complexed with Inhibitor Compound 24a
ComponentsArginase-1
KeywordsHYDROLASE/INHIBITOR / Arginase / hydrolase / urea cycle / metabolism / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Chem-0IZ / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPalte, R.L.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Structure-Based Discovery of Proline-Derived Arginase Inhibitors with Improved Oral Bioavailability for Immuno-Oncology.
Authors: Lu, M. / Zhang, H. / Li, D. / Childers, M. / Pu, Q. / Palte, R.L. / Gathiaka, S. / Lyons, T.W. / Palani, A. / Fan, P.W. / Spacciapoli, P. / Miller, J.R. / Cho, H. / Cheng, M. / Chakravarthy, ...Authors: Lu, M. / Zhang, H. / Li, D. / Childers, M. / Pu, Q. / Palte, R.L. / Gathiaka, S. / Lyons, T.W. / Palani, A. / Fan, P.W. / Spacciapoli, P. / Miller, J.R. / Cho, H. / Cheng, M. / Chakravarthy, K. / O'Neil, J. / Eangoor, P. / Beard, A. / Kim, H.Y. / Sauri, J. / Gunaydin, H. / Sloman, D.L. / Siliphaivanh, P. / Cumming, J. / Fischer, C.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginase-1
B: Arginase-1
C: Arginase-1
D: Arginase-1
E: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,33224
Polymers208,6796
Non-polymers2,65218
Water15,709872
1
A: Arginase-1
B: Arginase-1
E: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,66612
Polymers104,3403
Non-polymers1,3269
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Arginase-1
D: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,66612
Polymers104,3403
Non-polymers1,3269
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.680, 289.270, 67.430
Angle α, β, γ (deg.)90.000, 90.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arginase-1 / Liver-type arginase / Type I arginase


Mass: 34779.879 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-0IZ / 3-[(2~{S},3~{R},4~{R})-4-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron


Mass: 332.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H27BN3O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O
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: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MMT (pH 7.0), 0.1 M ammonium formate, 16-22% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→72.32 Å / Num. obs: 92463 / % possible obs: 98.3 % / Redundancy: 3.3 % / CC1/2: 0.988 / Net I/σ(I): 7.5
Reflection shellResolution: 2.27→2.4 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 13581 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7C

6v7c


Resolution: 2.27→72.32 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.81 / SU R Cruickshank DPI: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.325 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4579 4.96 %RANDOM
Rwork0.203 ---
obs0.205 92396 98 %-
Displacement parametersBiso max: 115.65 Å2 / Biso mean: 28.62 Å2 / Biso min: 4.67 Å2
Baniso -1Baniso -2Baniso -3
1-6.749 Å20 Å23.4642 Å2
2---16.9765 Å20 Å2
3---10.2275 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.27→72.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14454 0 150 872 15476
Biso mean--25.84 28.06 -
Num. residues----1902
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5172SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2154HARMONIC5
X-RAY DIFFRACTIONt_it14892HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1980SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17866SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14892HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20214HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.27→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2849 340 5.1 %
Rwork0.2203 6331 -
all0.2235 6671 -
obs--94.98 %

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