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- PDB-1i76: COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLIN... -

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Basic information

Entry
Database: PDB / ID: 1i76
TitleCOMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (D-TIC DERIVATIVE) WITH T CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
ComponentsNEUTROPHIL COLLAGENASE
KeywordsHYDROLASE / COMPLEX (METALLOPROTEASE-INHIBITOR)
Function / homology
Function and homology information


neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / collagen-containing extracellular matrix / endopeptidase activity / cellular response to lipopolysaccharide / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BSI / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A.
Citation
Journal: J.Med.Chem. / Year: 2000
Title: Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design.
Authors: Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A.
#1: Journal: J.Med.Chem. / Year: 1999
Title: QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP OF HUMAN NEUTROPHIL COLLAGENASE (MMP8-8) INHIBITORS USING COMPARATIVE MOLECULAR FIELD ANALYSIS AND X-RAY STRUCTURE ANALYSIS
Authors: Matter, H. / Schwab, W. / Barbier, D. / Billen, G. / Haase, B. / Schudok, M. / Neises, B. / Thorwart, W. / Schreuder, H. / Brachvogel, V. / Weithmann, K.U. / Loenze, P.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: X-RAY STRUCTURES OF HUMAN NEUTROPHIL COLLAGENASE COMPLEXED WITH PEPTIDE HYDROXAMATE AND PEPTIDE THIOL INHIBITORS. IMPLICATIONS FOR SUBSTRATE BINDING AND RATIONAL DRUG DESIGN
Authors: Grams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Pieper, M. / Tschesche, H. / Huber, R. / Bode, W.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 9, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7166
Polymers18,1121
Non-polymers6045
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.990, 68.684, 70.584
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 NEUTROPHIL COLLAGENASE / / MATRIX METALLOPROTEINASE-8 / MMP-8


Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22894, neutrophil collagenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BSI / 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID


Mass: 393.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19NO4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES-NAOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Details: 2 micro litte of protein solution, 1 miro litter of inhibitor solution, and 5 micro litter of PEG solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
25 mM1dropCaCl2
3100 mM1dropNaCl
40.5 mM1dropZnCl2
53 mMMES-NaOH1drop
620 mMinhibitor1dropin 0.2 M MES-NaOH, 0.02 % NaN3, pH 6.0
710 %(v/v)PEG60001drop0.2 M MES-NaOH, 0.2 M MES-NaOH, 0.02 % NaN3, pH 6.0
82.0 Msodium phosphate1reservoir
90.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 21, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 51100 / Num. obs: 50709 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.6
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 411807
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JAP

1jap


Resolution: 1.2→10 Å / Num. parameters: 14352 / Num. restraintsaints: 17304 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2521 10 %RANDOM
Rwork0.129 ---
all0.1317 48054 --
obs0.1317 48054 --
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 1201 / Occupancy sum non hydrogen: 1586
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 32 271 1617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.293
X-RAY DIFFRACTIONs_zero_chiral_vol0.15
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
LS refinement shellResolution: 1.2→10 Å
RfactorNum. reflection
Rfree0.171 2521
Rwork0.129 -
obs-48054

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