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- PDB-1gkc: MMP9-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 1gkc
TitleMMP9-inhibitor complex
Components92 KDA TYPE IV COLLAGENASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MATRIX METALLOPROTEASE / HYDROLASE / GLYCOPROTEIN / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / 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 / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of 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-NFH / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 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_site
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.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_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

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)38,06218
Polymers36,7692
Non-polymers1,29316
Water2,162120
1
A: 92 KDA TYPE IV COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0319
Polymers18,3841
Non-polymers6478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 92 KDA TYPE IV COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0319
Polymers18,3841
Non-polymers6478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.005, 56.005, 262.655
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: (-0.22861, -0.9625, 0.14604), (-0.95777, 0.19549, -0.21085), (0.1744, -0.18808, -0.96655)
Vector: 68.09161, 96.29951, 249.65909)

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Components

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


Mass: 18384.408 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN RESIDUES 107-215,391-443
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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NFH / N~2~-[(2R)-2-{[formyl(hydroxy)amino]methyl}-4-methylpentanoyl]-N,3-dimethyl-L-valinamide


Mass: 315.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29N3O4
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF PURIFIED COMPLEX SOLUTION (0.55 MG/ML PROTEIN AND 0.5 MM INHIBITOR SOLUTION CONCENTRATED TO ~4 MG/ML IN 20 MM TRIS- HCL PH 7.5, 2 MM ...Details: THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF PURIFIED COMPLEX SOLUTION (0.55 MG/ML PROTEIN AND 0.5 MM INHIBITOR SOLUTION CONCENTRATED TO ~4 MG/ML IN 20 MM TRIS- HCL PH 7.5, 2 MM CACL2, 50 MM NACL) AND RESERVOIR BUFFER (3.6 M NACL, 0.1 M HEPES PH 7.5).
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.55 mg/mlprotein1drop
20.5 mMinhibitor1drop
320 mMTris-HCl1droppH7.5
42 mM1dropCaCl2
550 mM1dropNaCl
63.6 M1reservoirNaCl
70.1 MHEPES1reservoirpH7.5

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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 25, 1999 / 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: 2.3→51.3 Å / Num. obs: 17375 / % possible obs: 88 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.479 / % possible all: 83
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 88.3 % / Num. measured all: 77726
Reflection shell
*PLUS
% possible obs: 83.3 % / Num. unique obs: 2656 / Num. measured obs: 10147

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Processing

Software
NameVersionClassification
CNX2000refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFS

1hfs


Resolution: 2.3→51.3 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR, CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 684 3.5 %RANDOM
Rwork0.207 ---
obs-17375 88.3 %-
Solvent computationSolvent model: MASK / Bsol: 47.85 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--5.43 Å20 Å20 Å2
2---5.43 Å20 Å2
3---10.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 58 120 2690
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it2.672
X-RAY DIFFRACTIONc_scangle_it3.862.5
Refine LS restraints NCSRms dev Biso : 2.6 Å2 / Rms dev position: 0.09 Å / Weight Biso : 2 / Weight position: 50
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 68 3.6 %
Rwork0.277 1517 -
obs--83 %
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: 2.3 Å / Lowest resolution: 51.3 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_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor obs: 0.277

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