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- PDB-1i73: COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF... -

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Basic information

Entry
Database: PDB / ID: 1i73
TitleCOMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
Components
  • NEUTROPHIL COLLAGENASE
  • THREE RESIDUE PEPTIDE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEASE-INHIBITOR complex / HYDROLASE-HYDROLASE INHIBITOR complex
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 / : / cellular response to lipopolysaccharide / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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
Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: 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.
#2: 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. / Neises, B. / Schudok, M. / Thorwart, W. / Schreuder, H. / Brachvogel, V. / Loenze, P. / Weithmann, K.U.
History
DepositionMar 7, 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: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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
B: THREE RESIDUE PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8176
Polymers18,6062
Non-polymers2114
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-67 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.983, 68.673, 70.486
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: Protein/peptide THREE RESIDUE PEPTIDE INHIBITOR


Mass: 494.478 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The three residue peptide inhibitor was chemically synthesized
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
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: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 32394 / Num. obs: 30229 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.1 / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 106034
Reflection shell
*PLUS
% possible obs: 85.6 %

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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: 1.4→10 Å / Num. parameters: 14472 / Num. restraintsaints: 17466 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1508 10 %RANDOM
Rwork0.1341 ---
all0.1376 28619 --
obs0.1376 28619 --
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1203 / Occupancy sum non hydrogen: 1589
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 4 281 1599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.307
X-RAY DIFFRACTIONs_zero_chiral_vol0.152
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
LS refinement shellResolution: 1.4→10 Å
RfactorNum. reflection
Rfree0.194 1508
Rwork0.1341 -
obs-28619

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