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- PDB-7k4j: Human Arginase 1 in complex with compound 51. -

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Basic information

Entry
Database: PDB / ID: 7k4j
TitleHuman Arginase 1 in complex with compound 51.
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE inhibitor / Arginase / hydrolase / arginine / urea cycle / inhibitor / HYDROLASE-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-VV1 / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPalte, R.L.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors.
Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, ...Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, L. / Gathiaka, S. / Sauri, J. / Kim, H.Y. / Adpressa, D. / Spacciapoli, P. / Miller, J.R. / Palte, R.L. / Lesburg, C.A. / Cumming, J. / Fischer, C.
History
DepositionSep 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 2.0Dec 8, 2021Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 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)210,80924
Polymers208,6796
Non-polymers2,13018
Water16,628923
1
A: Arginase-1
B: Arginase-1
E: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,40412
Polymers104,3403
Non-polymers1,0659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-18 kcal/mol
Surface area33420 Å2
MethodPISA
2
C: Arginase-1
D: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,40412
Polymers104,3403
Non-polymers1,0659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-15 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 287.060, 67.380
Angle α, β, γ (deg.)90.000, 90.110, 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-VV1 / 3-[(1~{S},2~{S},5~{R})-2-carboxy-3,6-diazabicyclo[3.2.0]heptan-1-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide


Mass: 245.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H18BN2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
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 80

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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: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→67.38 Å / Num. obs: 131620 / % possible obs: 88.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.9
Reflection shellResolution: 1.94→2.05 Å / Num. unique obs: 19063 / CC1/2: 0.881

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7D

6v7d


Resolution: 1.94→67.38 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.813 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6488 4.93 %RANDOM
Rwork0.209 ---
obs0.212 131550 88.3 %-
Displacement parametersBiso max: 110.39 Å2 / Biso mean: 24.73 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-6.4188 Å20 Å21.9088 Å2
2---15.8928 Å20 Å2
3---9.474 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.94→67.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14454 0 114 923 15491
Biso mean--19.9 26.79 -
Num. residues----1902
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5160SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2148HARMONIC5
X-RAY DIFFRACTIONt_it14862HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
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_contact18799SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14862HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20184HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.23
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2663 432 5.28 %
Rwork0.2297 7746 -
all0.2319 8178 -
obs--73.86 %

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