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- PDB-1wb0: specificity and affinity of natural product cyclopentapeptide inh... -

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Basic information

Entry
Database: PDB / ID: 1wb0
Titlespecificity and affinity of natural product cyclopentapeptide inhibitor Argifin against human chitinase
Components
  • ARGIFIN
  • CHITOTRIOSIDASE 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYCLOPENTAPEPTIDE INHIBITORS / CHITINASE INHIBITORS / CARBOHYDRATE METABOLISM / CHITIN DEGRADATION / CHITIN-BINDING / GLYCOSIDASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region
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 / Chitinase II ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Argifin / ISOPROPYL ALCOHOL / Chitotriosidase-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Hodkinson, M. / Adams, D.J. / Shiomi, K. / Omura, S. / Van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2005
Title: Specificity and Affinity of Natural Product Cyclopentapeptide Inhibitors Against Aspergillus Fumigatus, Human and Bacterial Chitinases
Authors: Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Hodkinson, M. / Adams, D.J. / Shiomi, K. / Omura, S. / Van Aalten, D.M.F.
History
DepositionOct 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITOTRIOSIDASE 1
B: ARGIFIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6548
Polymers50,1182
Non-polymers5366
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.286, 53.725, 134.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein CHITOTRIOSIDASE 1 / CHITINASE 1


Mass: 49424.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q13231, chitinase
#2: Protein/peptide ARGIFIN


Type: Oligopeptide / Class: Inhibitor / Mass: 693.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: Argifin

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Non-polymers , 4 types, 230 molecules

#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: DEGRADES CHITIN AND CHITOTRIOSE. MAY PARTICIPATE IN THE DEFENSE AGAINST NEMATODES AND ...FUNCTION: DEGRADES CHITIN AND CHITOTRIOSE. MAY PARTICIPATE IN THE DEFENSE AGAINST NEMATODES AND OTHER PATHOGENS. ISOFORM 3 HAS NO ENZYMATIC ACTIVITY. CATALYTIC ACTIVITY: HYDROLYSIS OF THE 1,4-BETA-LINKAGES OF N- ACETYL-D-GLUCOSAMINE POLYMERS OF CHITIN. SUBCELLULAR LOCATION: SECRETED. A SMALL PROPORTION IS LYSOSOMAL. TISSUE SPECIFICITY: DETECTED IN SPLEEN. SECRETED BY CULTURED MACROPHAGES. SIMILARITY: BELONGS TO THE GLYCOSYL HYDROLASE 18 FAMILY. CHITINASE CLASS II SUBFAMILY. SIMILARITY: CONTAINS 1 CHITIN-BINDING TYPE-2 DOMAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 40166 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.7 / % possible all: 83.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUV

1guv


Resolution: 1.65→24.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1446670 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.188 827 2.1 %RANDOM
Rwork0.178 ---
obs0.178 40113 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.15 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---0.87 Å20 Å2
3---2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.65→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 30 224 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 122 2.2 %
Rwork0.207 5533 -
obs--80.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ARGIFIN.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMARGIFIN.TOP
X-RAY DIFFRACTION5COMBINED.PARAMCOMBINED.TOP

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