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- PDB-3rm4: AMCase in complex with Compound 1 -

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Basic information

Entry
Database: PDB / ID: 3rm4
TitleAMCase in complex with Compound 1
ComponentsAcidic mammalian chitinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process ...chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process / positive regulation of chemokine production / kinase binding / apoptotic process / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3RM / Acidic mammalian chitinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOlland, A.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Identification and Characterization of Acidic Mammalian Chitinase Inhibitors
Authors: Cole, D.C. / Olland, A.M. / Jacob, J. / Brooks, J. / Bursavich, M.G. / Czerwinski, R. / Declercq, C. / Johnson, M. / Joseph-McCarthy, D. / Ellingboe, J.W. / Lin, L. / Nowak, P. / Presman, E. ...Authors: Cole, D.C. / Olland, A.M. / Jacob, J. / Brooks, J. / Bursavich, M.G. / Czerwinski, R. / Declercq, C. / Johnson, M. / Joseph-McCarthy, D. / Ellingboe, J.W. / Lin, L. / Nowak, P. / Presman, E. / Strand, J. / Tam, A. / Williams, C.M.M. / Yao, S. / Tsao, D.H.H. / Fitz, L.J.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acidic mammalian chitinase
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1414
Polymers88,4072
Non-polymers7342
Water9,764542
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5712
Polymers44,2031
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5712
Polymers44,2031
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.498, 89.371, 126.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acidic mammalian chitinase / AMCase / Lung-specific protein TSA1902


Mass: 44203.371 Da / Num. of mol.: 2 / Fragment: catalytic domain residues 22-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIA / Cell line (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q9BZP6, chitinase
#2: Chemical ChemComp-3RM / 5-{4-[2-(4-bromophenoxy)ethyl]piperazin-1-yl}-4H-1,2,4-triazol-3-amine


Mass: 367.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19BrN6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→73 Å / Num. obs: 57725

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fy1

3fy1


Resolution: 1.9→29.917 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.247 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23018 2926 5.1 %RANDOM
Rwork0.18801 ---
obs0.19014 54767 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 44 542 6526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9398428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97424.898294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48215921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6011514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23045
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2487
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6541.53814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7925986
X-RAY DIFFRACTIONr_scbond_it1.69332808
X-RAY DIFFRACTIONr_scangle_it2.254.52442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 211 -
Rwork0.213 4015 -
obs--99.98 %
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)
10.47440.0615-0.14350.38470.03650.4738-0.01070.0191-0.045-0.01-0.00120.04760.0003-0.04010.0119-0.02140.0006-0.011-0.0212-0.0054-0.0298-7.828-3.078-19.812
20.472-0.2759-0.07870.28580.06650.45530.011-0.0118-0.0402-0.023-0.00740.0320.01180.0461-0.0037-0.0152-0.0058-0.0073-0.02780.0049-0.02297.977-1.3229.906
30.9293-0.30890.02941.27310.02771.2189-0.0537-0.01370.02950.08830.0343-0.1238-0.13820.10040.0194-0.0056-0.0249-0.0209-0.02770.0031-0.034814.32712.327-22.456
40.60330.0052-0.15751.0247-0.03150.56880.0550.0478-0.011-0.0679-0.04740.1576-0.0572-0.0846-0.0075-0.00570.0308-0.0053-0.0148-0.0119-0.0215-13.78514.9110.044
50.72260.2961-0.21630.96560.80511.40370.02760.16540.0912-0.07140.01790.0404-0.0567-0.146-0.0455-0.00460.0236-0.01050.00810.0309-0.0342-2.82210.437-31.996
60.8879-0.28210.07641.5509-0.56160.96940.0353-0.10010.06970.0795-0.0064-0.0641-0.12990.0351-0.0289-0.0052-0.01780.0052-0.0198-0.0176-0.02573.1713.77520.147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 267
2X-RAY DIFFRACTION2B22 - 267
3X-RAY DIFFRACTION3A268 - 338
4X-RAY DIFFRACTION4B268 - 338
5X-RAY DIFFRACTION5A339 - 394
6X-RAY DIFFRACTION6B339 - 394

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