[English] 日本語
Yorodumi
- PDB-7qft: Crystal structure of KLK6 in complex with compound 16a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qft
TitleCrystal structure of KLK6 in complex with compound 16a
Components
  • KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)
  • Kallikrein-6
KeywordsPEPTIDE BINDING PROTEIN / serine proteases
Function / homology
Function and homology information


cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intercellular bridge / myelination / secretory granule / protein maturation / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsJagtap, P.K.A. / Zhang, L. / De Vita, E. / Tate, E.W. / Hennig, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: A KLK6 Activity-Based Probe Reveals a Role for KLK6 Activity in Pancreatic Cancer Cell Invasion.
Authors: Zhang, L. / Lovell, S. / De Vita, E. / Jagtap, P.K.A. / Lucy, D. / Goya Grocin, A. / Kjaer, S. / Borg, A. / Hennig, J. / Miller, A.K. / Tate, E.W.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_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_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kallikrein-6
B: Kallikrein-6
C: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)
D: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)50,7664
Polymers50,7664
Non-polymers00
Water7,927440
1
A: Kallikrein-6
D: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,3832
Polymers25,3832
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
C: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,3832
Polymers25,3832
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.370, 39.970, 65.070
Angle α, β, γ (deg.)81.900, 84.950, 70.710
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 25 or resid 27...
d_2ens_1(chain "B" and (resid 16 through 25 or resid 27...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUTHRTHRAA16 - 251 - 10
d_12HISHISSERSERAA27 - 8312 - 66
d_13VALVALALAALAAA85 - 24468 - 222
d_14DPNDPNA1H2EA1H2EDD1 - 42 - 5
d_21LEULEUTHRTHRBB16 - 251 - 10
d_22HISHISSERSERBB27 - 8312 - 66
d_23VALVALALAALABB85 - 24468 - 222
d_24ACAACAA1H2EA1H2ECC1 - 51 - 5

-
Components

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


Mass: 24417.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Plasmid: pXLG / Production host: Homo sapiens (human) / Strain (production host): Expi293F
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Mass: 965.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20 M trimethylamine N-oxide, 0.1 M Tris-HCl pH8.5, 20% PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.47→64.36 Å / Num. obs: 57658 / % possible obs: 94.7 % / Redundancy: 3.407 % / Biso Wilson estimate: 16.13 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.097 / Χ2: 0.903 / Net I/σ(I): 9.2 / Num. measured all: 196458 / Scaling rejects: 132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.513.1731.2141.311333448135720.361.45179.7
1.51-1.553.4470.8841.9214302440341490.5621.04694.2
1.55-1.63.4660.6442.5114159432140850.6890.76294.5
1.6-1.653.4730.4723.3313415406538630.790.55895
1.65-1.73.450.3683.9413144401838100.860.43594.8
1.7-1.763.3620.2824.8312593392137460.9180.33495.5
1.76-1.833.1010.2185.7211194376736100.9350.26495.8
1.83-1.93.1790.1717.0410893360134270.9610.20795.2
1.9-1.993.4110.1289.3111311347533160.9760.15395.4
1.99-2.083.570.10411.1511270328531570.9830.12296.1
2.08-2.23.6140.08912.6911043315130560.9880.10597
2.2-2.333.50.08413.7110090298028830.9890.09996.7
2.33-2.493.5370.07514.589662281027320.990.08997.2
2.49-2.693.4510.06915.538715260425250.990.08297
2.69-2.953.3810.06316.777895239423350.9920.07597.5
2.95-3.33.1070.05417.866437215220720.9920.06696.3
3.3-3.813.2180.05119.975902193518340.9930.06294.8
3.81-4.663.7310.0522.975839159215650.9950.05998.3
4.66-6.593.8140.0523.234771126412510.9870.05899
6.59-64.363.7160.04523.624906766700.9950.05399.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VFE

3vfe


Resolution: 1.47→64.36 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.3781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 2881 5 %
Rwork0.1719 54762 -
obs0.1735 57643 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.47→64.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 109 440 3914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743582
X-RAY DIFFRACTIONf_angle_d1.2374875
X-RAY DIFFRACTIONf_chiral_restr0.102530
X-RAY DIFFRACTIONf_plane_restr0.0083632
X-RAY DIFFRACTIONf_dihedral_angle_d13.7667613
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.20597819608 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.51191010.43161942X-RAY DIFFRACTION71.94
1.5-1.520.38331380.30282608X-RAY DIFFRACTION93.34
1.52-1.550.28931360.26752593X-RAY DIFFRACTION94.33
1.55-1.580.27451360.24312572X-RAY DIFFRACTION94.42
1.58-1.610.24491390.2352649X-RAY DIFFRACTION95.15
1.61-1.650.24981360.23272585X-RAY DIFFRACTION94.54
1.65-1.690.29411400.22082656X-RAY DIFFRACTION95.23
1.69-1.730.25661380.21022618X-RAY DIFFRACTION95.13
1.73-1.780.21791370.18852607X-RAY DIFFRACTION95.61
1.78-1.830.22121400.17612672X-RAY DIFFRACTION95.91
1.83-1.890.20191380.17992607X-RAY DIFFRACTION95.05
1.89-1.960.21231370.17012602X-RAY DIFFRACTION94.97
1.96-2.030.22111410.16452677X-RAY DIFFRACTION96.54
2.03-2.130.21271400.16442662X-RAY DIFFRACTION96.12
2.13-2.240.2221390.16182656X-RAY DIFFRACTION96.81
2.24-2.380.20231420.16272695X-RAY DIFFRACTION97.12
2.38-2.560.23861400.16622654X-RAY DIFFRACTION97.12
2.56-2.820.17841400.16782683X-RAY DIFFRACTION97.28
2.82-3.230.16861410.16112675X-RAY DIFFRACTION97
3.23-4.070.15761380.13592626X-RAY DIFFRACTION95.47
4.07-64.360.16621440.15262723X-RAY DIFFRACTION98.83

+
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