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- PDB-4h3x: Crystal structure of an MMP broad spectrum hydroxamate based inhi... -

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Basic information

Entry
Database: PDB / ID: 4h3x
TitleCrystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE/HYDROLASE Inhibitor / HYDROLASE/HYDROXAMATE INHIBITOR / Zincin-like / Gelatinase / Collagenase (Catalytic Domain) / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of release of cytochrome c from mitochondria / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / macrophage differentiation / collagen catabolic process / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / positive regulation of protein phosphorylation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / 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
Chem-10B / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å
AuthorsStura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Dive, V. / Rossello, A.
Citation
Journal: J.Struct.Biol. / Year: 2013
Title: Crystallization of bi-functional ligand protein complexes.
Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A.
#1: Journal: J.Struct.Biol. / Year: 2013
Title: Crystallization of bi-functional ligand protein complexes.
Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4May 31, 2017Group: Structure summary
Revision 1.5Sep 20, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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_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_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 metalloproteinase-9
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,84124
Polymers36,6772
Non-polymers2,16422
Water6,846380
1
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,58214
Polymers18,3381
Non-polymers1,24413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,25810
Polymers18,3381
Non-polymers9209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 97.940, 46.080
Angle α, β, γ (deg.)90.00, 111.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Matrix metalloproteinase-9 / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB


Mass: 18338.318 Da / Num. of mol.: 2
Fragment: human wild-type MMP-9 catalytic domain unp residues 107-215/391-443
Mutation: E402Q,E402Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3 star) / References: UniProt: P14780, gelatinase B

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Non-polymers , 7 types, 402 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-10B / N-2-(biphenyl-4-ylsulfonyl)-N-2-(isopropyloxy)-acetohydroxamic acid / N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(propan-2-yloxy)glycinamide


Mass: 364.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N2O5S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO A CHIMERIC CONSTRUCT OBTAINED BY DELETING THE DOMAIN ...THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A CHIMERIC CONSTRUCT OBTAINED BY DELETING THE DOMAIN CORRESPONDING TO UNP RESIDUES 215-390

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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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: ...Details: protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 50/50, 200mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2011 / Details: bent cylindrical mirror
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 32612 / Num. obs: 31957 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.23 % / Biso Wilson estimate: 24.441 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.119 / Net I/σ(I): 8.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.76-1.874.130.6662.3352460.58294.2
1.87-24.280.4493.749810.39498.2
2-2.164.290.285.7945440.24598.7
2.16-2.374.270.217.1942360.18498.6
2.37-2.644.260.1579.2738480.13898.8
2.64-3.054.250.11512.0933960.198.9
3.05-3.734.220.0915.7328620.07899.1
3.73-5.264.180.0818.0322290.0799.1
5.26-504.130.07318.0612700.06399

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2E

4h2e


Resolution: 1.764→42.806 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 1598 5 %RANDOM
Rwork0.1964 ---
obs0.1993 31949 98.28 %-
all-31957 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.764→42.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 121 380 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072957
X-RAY DIFFRACTIONf_angle_d1.034030
X-RAY DIFFRACTIONf_dihedral_angle_d18.4511069
X-RAY DIFFRACTIONf_chiral_restr0.074385
X-RAY DIFFRACTIONf_plane_restr0.006533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7642-1.82110.31171370.26962598259892
1.8211-1.88620.30881430.23432723272398
1.8862-1.96180.25851450.20772754275499
1.9618-2.0510.24441450.22748274898
2.051-2.15920.2381450.18752769276999
2.1592-2.29440.26031470.19842788278899
2.2944-2.47160.31391460.19692762276299
2.4716-2.72030.23591460.19912789278999
2.7203-3.11380.28361460.19612776277699
3.1138-3.92260.22121480.176428072807100
3.9226-42.81810.23331500.189228372837100

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