[English] 日本語
Yorodumi
- PDB-6skd: Crystal Structure of Human Kallikrein 6 (I218Y) in complex with G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6skd
TitleCrystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK3397892A
ComponentsKallikrein-6KLK6
KeywordsHYDROLASE / Protease / Inhibitor / Complex
Function / homology
Function and homology information


tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
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 ...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 / Mainly Beta
Similarity search - Domain/homology
Chem-LH2 / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsThorpe, J.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Design and development of a series of borocycles as selective, covalent kallikrein 5 inhibitors.
Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / ...Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / Polyakova, O. / Smith, K.J. / Thomas, P. / Thorpe, J.H. / Trottet, L. / Wang, Y. / Hovnanian, A.
History
DepositionAug 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: 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-6
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7108
Polymers48,9352
Non-polymers7746
Water2,072115
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7633
Polymers24,4681
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9475
Polymers24,4681
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.030, 46.240, 80.440
Angle α, β, γ (deg.)90.000, 98.580, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Kallikrein-6 / KLK6 / Neurosin / Protease M / SP59 / Serine protease 18 / Serine protease 9 / Zyme


Mass: 24467.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-LH2 / 4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide


Mass: 295.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18BN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.26→23.12 Å / Num. all: 57724 / Num. obs: 19365 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 47.35 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.074 / Rrim(I) all: 0.133 / Net I/σ(I): 7.2
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1409 / CC1/2: 0.764 / Rpim(I) all: 0.506 / Rrim(I) all: 0.885 / % possible all: 93.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 2.26→23.12 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.439 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.439 / SU Rfree Blow DPI: 0.275 / SU Rfree Cruickshank DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.282 926 4.82 %RANDOM
Rwork0.224 ---
obs0.227 19226 95.9 %-
Displacement parametersBiso max: 126.85 Å2 / Biso mean: 43.63 Å2 / Biso min: 18.13 Å2
Baniso -1Baniso -2Baniso -3
1-9.4175 Å20 Å2-1.1861 Å2
2--6.3593 Å20 Å2
3----15.7768 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.26→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 58 115 3571
Biso mean--46.48 39.71 -
Num. residues----444
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1196SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes608HARMONIC5
X-RAY DIFFRACTIONt_it3586HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3905SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3586HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4872HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion19.12
LS refinement shellResolution: 2.26→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 46
RfactorNum. reflection% reflection
Rfree0.3198 15 3.59 %
Rwork0.2592 403 -
all0.2619 418 -
obs--93.06 %

+
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