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- PDB-1jap: COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF... -

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Basic information

Entry
Database: PDB / ID: 1jap
TitleCOMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
Components
  • MATRIX METALLO PROTEINASE-8 (MET80 FORM)
  • PRO-LEU-GLY-HYDROXYLAMINE
KeywordsCOMPLEX (METALLOPROTEASE/INHIBITOR) / METALLOPROTEASE / ZINC-ENDOPEPTIDASE / METZINCINS / COMPLEX (METALLOPROTEASE-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
L-prolyl-L-leucyl-N-hydroxyglycinamide / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.82 Å
AuthorsBode, W. / Reinemer, P. / Huber, R. / Kleine, T. / Schnierer, S. / Tschesche, H.
Citation
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.
#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: 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: Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Jun 5, 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_conn_type / 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.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: MATRIX METALLO PROTEINASE-8 (MET80 FORM)
I: PRO-LEU-GLY-HYDROXYLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6236
Polymers18,4122
Non-polymers2114
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-62 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.090, 69.370, 72.480
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-PHE79 FORM


Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 86 - 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: Protein/peptide PRO-LEU-GLY-HYDROXYLAMINE


Type: Peptide-like / Class: Inhibitor / Mass: 300.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: L-prolyl-L-leucyl-N-hydroxyglycinamide
#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.: 148 / 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
112 mg/mlprotein1dropcontained 0.0015ml protein solution
25 mM1dropcontained 0.0015ml protein solutionCaCl2
3100 mM1dropcontained 0.0015ml protein solutionNaCl
43 mMMES-NaOH1dropcontained 0.0015ml protein solution
50.02 %1dropcontained 0.0015ml protein solutionNaN3
650 mMPro-Leu-Gly-NHOH1dropcontained 0.002ml inhibitor solution
70.2 MMES-NaOH1dropcontained 0.002ml inhibitor solution
80.02 %1dropcontained 0.002ml inhibitor solutionNaN3
910 %(m/v)PEG60001dropcontained 0.006ml PEG solution
100.2 MMES-NaOH1dropcontained 0.006ml PEG solution
110.02 %1dropcontained 0.006ml PEG solutionNaN3
121 Mpotassium phosphate1reservoircontained 0.006ml PEG solution
130.02 %1reservoircontained 0.006ml PEG solutionNaN3

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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: 1.82→20 Å / Num. obs: 13898 / % possible obs: 89.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 1.82→2 Å / % possible all: 89.9

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
RefinementResolution: 1.82→6 Å /
RfactorNum. reflection
Rwork0.194 -
obs0.194 13520
Refinement stepCycle: LAST / Resolution: 1.82→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 2 148 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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

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