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- PDB-1gkd: MMP9 active site mutant-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 1gkd
TitleMMP9 active site mutant-inhibitor complex
Components92 KDA TYPE IV COLLAGENASE
KeywordsHYDROLASE / MATRIX METALLOPROTEASE / GLYCOPROTEIN
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / : / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of epidermal growth factor receptor signaling pathway ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / : / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of epidermal growth factor receptor signaling pathway / Activation of Matrix Metalloproteinases / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / collagen catabolic process / macrophage differentiation / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / collagen binding / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / embryo implantation / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / positive regulation of protein phosphorylation / metallopeptidase activity / tertiary granule lumen / cell migration / peptidase activity / : / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / 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 / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINO-N,3,3-TRIMETHYLBUTANAMIDE / Chem-STN / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRowsell, S. / Pauptit, R.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Mmp9 in Complex with a Reverse Hydroxamate Inhibitor
Authors: Rowsell, S. / Hawtin, P. / Minshull, C.A. / Jepson, H. / Brockbank, S. / Barratt, D. / Slater, A.M. / Mcpheat, W. / Waterson, D. / Henney, A. / Pauptit, R.A.
History
DepositionAug 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_conn_type
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 92 KDA TYPE IV COLLAGENASE
B: 92 KDA TYPE IV COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01618
Polymers36,7672
Non-polymers1,24916
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.523, 56.523, 263.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.21819, -0.95291, -0.21059), (-0.9582, -0.25011, 0.13893), (-0.18506, 0.17148, -0.96765)
Vector: 34.527, 44.13337, -0.73378)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 92 KDA TYPE IV COLLAGENASE / MMP-9 / 92 KDA GELATINASE / GELATINASE B / MATRIX METALLOPROTEINASE-9


Mass: 18383.424 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN RESIDUES 107-215,391-443 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14780, gelatinase B

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Non-polymers , 5 types, 200 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-STN / 2-{[FORMYL(HYDROXY)AMINO]METHYL}-4-METHYLPENTANOIC ACID


Mass: 189.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4
#4: Chemical ChemComp-BUM / 2-AMINO-N,3,3-TRIMETHYLBUTANAMIDE


Mass: 144.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE INITIAL METHIONINE IN THE MATERIAL CRYSTALLISED IS A CLONING ARTEFACT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 50 %
Crystal growpH: 9
Details: PROTEIN SOLUTION (4MG/ML IN 20MM TRIS-HCL PH 7.5, 50MM NACL) WAS INCUBATED WITH 5MM INHIBITOR FOR 30MINS PRIOR TO SETTING UP CRYSTALLISATION TRIALS. THE CRYSTALLISATION DROPS CONTAINED A 1:1 ...Details: PROTEIN SOLUTION (4MG/ML IN 20MM TRIS-HCL PH 7.5, 50MM NACL) WAS INCUBATED WITH 5MM INHIBITOR FOR 30MINS PRIOR TO SETTING UP CRYSTALLISATION TRIALS. THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR BUFFER (2.6 - 2.8 M NACL, 0.1 M HEPES PH 9.0).
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
350 mM1dropNaCl
45.0 mMinhibitor1drop
52.6-2.8 M1reservoirNaCl
60.1 MHEPES1reservoirpH9.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 22, 2000 / Details: SILICON MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→36.3 Å / Num. obs: 18276 / % possible obs: 70 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.27 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.385 / % possible all: 40
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 71.2 % / Num. measured all: 50609
Reflection shell
*PLUS
% possible obs: 40.4 % / Num. unique obs: 2038 / Num. measured obs: 3391

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Processing

Software
NameVersionClassification
CNX2000refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE MMP-9 STRUCTURE (1GKC)

1gkc


Resolution: 2.1→36.3 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1439 5.5 %RANDOM
Rwork0.212 ---
obs-18276 69.9 %-
Solvent computationSolvent model: MASK / Bsol: 58.27 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--4.81 Å20 Å20 Å2
2---4.81 Å20 Å2
3---9.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 56 184 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.142
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it1.782.5
Refine LS restraints NCSRms dev Biso : 1.08 Å2 / Rms dev position: 0.1 Å / Weight Biso : 2 / Weight position: 50
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 52 2 %
Rwork0.266 696 -
obs--29 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4FRA.PARFRA.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 36.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor obs: 0.266

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