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- PDB-4ilw: Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd... -

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Basic information

Entry
Database: PDB / ID: 4ilw
TitleComplex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-2 (TIMP-2)
Components
  • Metalloproteinase inhibitor 2
  • Stromelysin-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Metzincin / OB-fold / Metalloproteinase / Protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


stromelysin 2 / negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...stromelysin 2 / negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / response to hormone / response to cytokine / metalloendopeptidase activity / specific granule lumen / tertiary granule lumen / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Stromelysin-2 / Metalloproteinase inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsBatra, J. / Soares, A.S. / Radisky, E.S.
CitationJournal: Plos One / Year: 2013
Title: Matrix Metalloproteinase-10/TIMP-2 Structure and Analyses Define Conserved Core Interactions and Diverse Exosite Interactions in MMP/TIMP Complexes.
Authors: Batra, J. / Soares, A.S. / Mehner, C. / Radisky, E.S.
History
DepositionJan 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Metalloproteinase inhibitor 2
B: Metalloproteinase inhibitor 2
D: Stromelysin-2
F: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,20914
Polymers80,7074
Non-polymers50210
Water2,882160
1
A: Metalloproteinase inhibitor 2
D: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6057
Polymers40,3542
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-79 kcal/mol
Surface area15890 Å2
MethodPISA
2
B: Metalloproteinase inhibitor 2
F: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6057
Polymers40,3542
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-76 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.687, 56.934, 82.592
Angle α, β, γ (deg.)76.14, 79.84, 71.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSALAALAAA1 - 1821 - 182
21CYSCYSALAALABB1 - 1821 - 182
12METMETGLYGLYDC105 - 2637 - 165
22METMETGLYGLYFD105 - 2637 - 165

NCS ensembles :
ID
1
2

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Components

#1: Protein Metalloproteinase inhibitor 2 / CSC-21K / Tissue inhibitor of metalloproteinases 2 / TIMP-2


Mass: 21783.039 Da / Num. of mol.: 2 / Fragment: Tissue inhibitor of metalloproteinases-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP2 / Plasmid: pTT/TIMP2 / Cell line (production host): HEK 293E / Production host: Homo sapiens (human) / References: UniProt: P16035
#2: Protein Stromelysin-2 / SL-2 / Matrix metalloproteinase-10 / MMP-10 / Transin-2


Mass: 18570.561 Da / Num. of mol.: 2 / Fragment: Matrix metalloproteinase-10 catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP-10, MMP10, STMY2 / Plasmid: MMP-10cd cDNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09238, stromelysin 2
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 25 % (w/v) PEG 2000 MME, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 35606 / Num. obs: 35606 / % possible obs: 97.66 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.415 / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V96, 1BR9

3v96

1br9


Resolution: 2.103→40.58 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.098 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26305 1782 5 %RANDOM
Rwork0.21632 ---
obs0.21873 35606 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20.7 Å2-0.18 Å2
2---1.89 Å2-0.97 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.103→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 10 160 5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195556
X-RAY DIFFRACTIONr_bond_other_d0.0050.025104
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9447544
X-RAY DIFFRACTIONr_angle_other_deg1.1453.00411794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6885686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52224.375256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36415914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2731522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216290
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021276
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101670.14
12B101670.14
21D92350.09
22F92350.09
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 133 -
Rwork0.278 2286 -
obs--90.36 %

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