[English] 日本語
Yorodumi
- PDB-6kbr: Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kbr
TitleCrystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex
Components
  • K41043
  • Kallikrein-4KLK4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein engineering / Cystine knot protein / Protease inhibitor / Structural analysis / PROTEIN BINDING / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / spermatid development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / acrosomal vesicle / secretory granule ...biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / spermatid development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / acrosomal vesicle / secretory granule / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Serine protease inhibitor Kazal-type 2 / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site ...Serine protease inhibitor Kazal-type 2 / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease inhibitor Kazal-type 2 / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKawaguchi, Y. / Nishimiya, D.
CitationJournal: Sci Rep / Year: 2019
Title: A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases.
Authors: Nishimiya, D. / Kawaguchi, Y. / Kodama, S. / Nasu, H. / Yano, H. / Yamaguchi, A. / Tamura, M. / Hashimoto, R.
History
DepositionJun 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kallikrein-4
C: K41043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4003
Polymers34,3082
Non-polymers921
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.208, 41.620, 43.590
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Kallikrein-4 / KLK4 / Enamel matrix serine proteinase 1 / Kallikrein-like protein 1 / KLK-L1 / Prostase / Serine protease 17


Mass: 27048.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Production host: Homo sapiens (human)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein K41043 / SPINK2


Mass: 7259.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Origami vector p7308 (others) / References: UniProt: P20155*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Lithium chloride, polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→72.577 Å / Num. obs: 20687 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 1283

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDG

2bdg


Resolution: 2→72.577 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.053 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22584 897 5 %RANDOM
Rwork0.18541 ---
obs0.18747 16901 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.645 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→72.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 6 110 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192137
X-RAY DIFFRACTIONr_bond_other_d0.0020.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9522904
X-RAY DIFFRACTIONr_angle_other_deg1.09234533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47725.05787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18115339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.053158
X-RAY DIFFRACTIONr_chiral_restr0.120.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212445
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02469
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0550.9521110
X-RAY DIFFRACTIONr_mcbond_other1.0540.9481109
X-RAY DIFFRACTIONr_mcangle_it1.7311.4141384
X-RAY DIFFRACTIONr_mcangle_other1.731.4181385
X-RAY DIFFRACTIONr_scbond_it1.7051.1511027
X-RAY DIFFRACTIONr_scbond_other1.7051.1511027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7041.6461521
X-RAY DIFFRACTIONr_long_range_B_refined3.9087.812415
X-RAY DIFFRACTIONr_long_range_B_other3.9077.8122416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 72 -
Rwork0.185 1211 -
obs--99.77 %

+
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