[English] 日本語
Yorodumi
- PDB-1gkc: MMP9-inhibitor complex -

+
Open data


ID or keywords:

Loading...

-
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 / : / : / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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


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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more