[English] 日本語
Yorodumi
- PDB-7u5b: Structure of Human KLK5 bound to anti-KLK5 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u5b
TitleStructure of Human KLK5 bound to anti-KLK5 Fab
Components
  • Kallikrein-5
  • anti-KLK5 Fab Heavy Chain
  • anti-KLK5 Fab Light Chain
KeywordsHYDROLASE/IMMUNE SYSTEM / Protease / Kallikrien / KLK5 / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


cornification / positive regulation of antibacterial peptide production / epidermal lamellar body / amelogenesis / Formation of the cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development / serine-type peptidase activity ...cornification / positive regulation of antibacterial peptide production / epidermal lamellar body / amelogenesis / Formation of the cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development / serine-type peptidase activity / secretory granule / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.371 Å
AuthorsYin, J. / Sudhamsu, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Sci Transl Med / Year: 2022
Title: Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis.
Authors: Chavarria-Smith, J. / Chiu, C.P.C. / Jackman, J.K. / Yin, J. / Zhang, J. / Hackney, J.A. / Lin, W.Y. / Tyagi, T. / Sun, Y. / Tao, J. / Dunlap, D. / Morton, W.D. / Ghodge, S.V. / Maun, H.R. / ...Authors: Chavarria-Smith, J. / Chiu, C.P.C. / Jackman, J.K. / Yin, J. / Zhang, J. / Hackney, J.A. / Lin, W.Y. / Tyagi, T. / Sun, Y. / Tao, J. / Dunlap, D. / Morton, W.D. / Ghodge, S.V. / Maun, H.R. / Li, H. / Hernandez-Barry, H. / Loyet, K.M. / Chen, E. / Liu, J. / Tam, C. / Yaspan, B.L. / Cai, H. / Balazs, M. / Arron, J.R. / Li, J. / Wittwer, A.J. / Pappu, R. / Austin, C.D. / Lee, W.P. / Lazarus, R.A. / Sudhamsu, J. / Koerber, J.T. / Yi, T.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-KLK5 Fab Heavy Chain
B: anti-KLK5 Fab Light Chain
H: anti-KLK5 Fab Heavy Chain
J: Kallikrein-5
L: anti-KLK5 Fab Light Chain
I: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,87321
Polymers144,4326
Non-polymers1,44115
Water2,198122
1
A: anti-KLK5 Fab Heavy Chain
B: anti-KLK5 Fab Light Chain
J: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,88810
Polymers72,2163
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: anti-KLK5 Fab Heavy Chain
L: anti-KLK5 Fab Light Chain
I: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98511
Polymers72,2163
Non-polymers7698
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.686, 283.624, 295.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

-
Components

#1: Antibody anti-KLK5 Fab Heavy Chain


Mass: 23659.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody anti-KLK5 Fab Light Chain


Mass: 23363.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Kallikrein-5 / / Kallikrein-like protein 2 / KLK-L2 / Stratum corneum tryptic enzyme


Mass: 25192.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK5, SCTE, UNQ570/PRO1132 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9Y337, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15% PEG4K, 0.1 M MgSO4 and 0.1 M sodium citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9876 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 2.371→52.875 Å / Num. obs: 806688 / % possible obs: 99.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 56.31 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.4
Reflection shellResolution: 2.371→2.379 Å / Redundancy: 9.8 % / Num. unique obs: 2797 / CC1/2: 0.866 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX1.12-2829_finalrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSX

2psx


Resolution: 2.371→52.875 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 3498 4.96 %
Rwork0.2216 66989 -
obs0.224 70487 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.87 Å2 / Biso mean: 75.722 Å2 / Biso min: 32.12 Å2
Refinement stepCycle: final / Resolution: 2.371→52.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 75 122 9101
Biso mean--108.22 59.84 -
Num. residues----1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019213
X-RAY DIFFRACTIONf_angle_d1.2212521
X-RAY DIFFRACTIONf_chiral_restr0.0651402
X-RAY DIFFRACTIONf_plane_restr0.0071581
X-RAY DIFFRACTIONf_dihedral_angle_d9.2526520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3711-2.40360.36531470.3167265099
2.4036-2.43790.33821450.30142669100
2.4379-2.47430.34791420.2787262099
2.4743-2.5130.27741210.2675268799
2.513-2.55420.31161050.2664269499
2.5542-2.59820.29991290.2638268799
2.5982-2.64550.35841300.2719266399
2.6455-2.69630.29251470.2537267499
2.6963-2.75140.33921210.2416265599
2.7514-2.81120.25391340.2369267599
2.8112-2.87660.28391560.24112669100
2.8766-2.94850.31381550.24352652100
2.9485-3.02820.26921340.2432267299
3.0282-3.11730.29251450.2484265398
3.1173-3.21790.33321370.2451250393
3.2179-3.33290.26321450.24432678100
3.3329-3.46640.29211350.23712712100
3.4664-3.62410.27461350.23232710100
3.6241-3.81510.28351420.23252726100
3.8151-4.0540.29461450.22032689100
4.054-4.36690.24341590.18692707100
4.3669-4.80610.25981470.17842731100
4.8061-5.50090.22251600.18942724100
5.5009-6.92820.26731600.2179260495
6.9282-52.8750.22111220.2114288599

+
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