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- PDB-7kll: Human Arginase1 Complexed with Inhibitor Compound 18 -

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Basic information

Entry
Database: PDB / ID: 7kll
TitleHuman Arginase1 Complexed with Inhibitor Compound 18
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 / arginine catabolic process to ornithine / arginase / 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 / arginine catabolic process to ornithine / arginase / 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-XFG / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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)210,73724
Polymers208,6796
Non-polymers2,05818
Water18,4291023
1
A: Arginase-1
B: Arginase-1
E: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,36812
Polymers104,3403
Non-polymers1,0299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Arginase-1
D: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,36812
Polymers104,3403
Non-polymers1,0299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.090, 287.140, 67.460
Angle α, β, γ (deg.)90.000, 90.380, 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-XFG / 3-[(2~{S},3~{R},4~{R})-4-azanyl-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron


Mass: 233.050 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18BN2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1023 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
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: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→95.71 Å / Num. obs: 95951 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.986 / Net I/σ(I): 7.7
Reflection shellResolution: 2.22→2.34 Å / Num. unique obs: 12583 / CC1/2: 0.704

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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: 2.22→71.79 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4754 4.97 %RANDOM
Rwork0.191 ---
obs0.193 95728 96.7 %-
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 24.81 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-2.7252 Å20 Å2-1.9524 Å2
2---10.1226 Å20 Å2
3---7.3974 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.22→71.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14454 0 108 1023 15585
Biso mean--20.69 26.47 -
Num. residues----1902
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2148HARMONIC5
X-RAY DIFFRACTIONt_it14850HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1974SEMIHARMONIC5
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_contact18428SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14850HARMONIC30.01
X-RAY DIFFRACTIONt_angle_deg20154HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion15.74
LS refinement shellResolution: 2.22→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3115 285 5.1 %
Rwork0.2276 5308 -
all0.2317 5593 -
obs--76.9 %

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