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- PDB-1jao: COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATA... -

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Basic information

Entry
Database: PDB / ID: 1jao
TitleCOMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
ComponentsMATRIX METALLO PROTEINASE-8 (MET80 FORM)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEASE / ZINC-ENDOPEPTIDASE / METZINCINS / 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
N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide / Chem-0D3 / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGrams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Piper, M. / Tschesche, H. / Huber, R. / Bode, W.
Citation
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.
#1: Journal: Embo J. / Year: 1994
Title: The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited by a Substrate Analogue Reveals the Essentials for Catalysis and Specificity
Authors: Bode, W. / Reinemer, P. / Huber, R. / Kleine, T. / Schnierer, S. / Tschesche, H.
#2: Journal: FEBS Lett. / Year: 1994
Title: Structural Implications for the Role of the N Terminus in the 'Superactivation' of Collagenases. A Crystallographic Study
Authors: Reinemer, P. / Grams, F. / Huber, R. / Kleine, T. / Schnierer, S. / Piper, M. / Tschesche, H. / Bode, W.
History
DepositionMar 11, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_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

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Assembly

Deposited unit
A: MATRIX METALLO PROTEINASE-8 (MET80 FORM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6466
Polymers18,1121
Non-polymers5345
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.240, 69.200, 72.330
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 MATRIX METALLO PROTEINASE-8 (MET80 FORM) / MMP-8-MET80 FORM


Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 80 - 242
Source method: isolated from a genetically manipulated source
Details: MMP-8 IS IDENTICAL TO THE HUMAN NEUTROPHIL COLLAGENASE
Source: (gene. exp.) Homo sapiens (human) / Cell: NEUTROPHILS / Production host: Escherichia coli (E. coli) / References: UniProt: P22894, neutrophil collagenase
#2: Chemical ChemComp-0D3 / N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 323.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N3O3S
References: N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide
#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.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 41 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlHNC solution1dropin 0.0018ml HNC solution
23 mMMES-NaOH1dropin 0.0018ml HNC solution
3100 mM1dropin 0.0018ml HNC solutionNaCl
45 mM1dropin 0.0018ml HNC solutionCaCl2
50.02 %1dropin 0.0018ml HNC solutionNaN3
690 mMSHBzlPp-AlaGly-NH21drop0.002ml
710 %(m/v)PEG60001dropin 0.006ml PEG solution
80.2 MMES-NaOH1dropin 0.006ml PEG solution
90.8 Mpotassium phosphate1reservoir
100.02 %1reservoirNaN3

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 6429 / % possible obs: 92.8 % / Rmerge(I) obs: 0.129
Reflection
*PLUS
Num. all: 20050 / Num. measured all: 20226
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å / % possible obs: 88 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 6409
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 26 95 1370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.43 Å / Rfactor Rwork: 0.254

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