[English] 日本語
Yorodumi
- PDB-6j8q: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j8q
TitleSerine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001
ComponentsSerine Beta-Lactamase KPC-2
KeywordsHYDROLASE / Beta-lactamase / Serine-beta-lactamase KPC-2 / KPC-2 / Carbapenemase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Chem-BHU / DI(HYDROXYETHYL)ETHER / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.787 Å
AuthorsLi, G.-B. / Liu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81874291; 81502989 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases.
Authors: Wang, Y.L. / Liu, S. / Yu, Z.J. / Lei, Y. / Huang, M.Y. / Yan, Y.H. / Ma, Q. / Zheng, Y. / Deng, H. / Sun, Y. / Wu, C. / Yu, Y. / Chen, Q. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionJan 21, 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.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine Beta-Lactamase KPC-2
B: Serine Beta-Lactamase KPC-2
C: Serine Beta-Lactamase KPC-2
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,27732
Polymers112,3184
Non-polymers2,95828
Water14,556808
1
A: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12011
Polymers28,0801
Non-polymers1,04010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
MethodPISA
2
B: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8018
Polymers28,0801
Non-polymers7227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10760 Å2
MethodPISA
3
C: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6256
Polymers28,0801
Non-polymers5455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area10950 Å2
MethodPISA
4
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7317
Polymers28,0801
Non-polymers6526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.159, 165.159, 94.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine Beta-Lactamase KPC-2 / Beta-lactamase


Mass: 28079.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Klebsiella pneumoniae / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase

-
Non-polymers , 5 types, 836 molecules

#2: Chemical
ChemComp-BHU / [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid / (S)-((3-mercapto-2-methylpropanamido)methyl)boronic acid


Mass: 177.030 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12BNO3S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)

-
Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 136404 / % possible obs: 97 % / Redundancy: 16.5 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.057 / Rrim(I) all: 0.228 / Χ2: 0.985 / Net I/σ(I): 3.1 / Num. measured all: 2249490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.78-1.845.7116330.1190.910.74683.4
1.84-1.929.4134740.2610.6380.76796.4
1.92-213.5136590.5310.4310.80298
2-2.1116.1137600.7240.3010.8498.1
2.11-2.2418.9137610.8740.2140.90598.60.9190.944
2.24-2.4219138690.9220.1580.99598.90.6790.697
2.42-2.6619.2138790.9580.1061.18698.70.4610.473
2.66-3.0420.2139730.9770.0731.38599.30.3230.331
3.04-3.8320.4140250.9860.0470.99299.10.2090.214
3.83-5020.4143710.990.0360.82799.30.1570.161

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.4 Å47.68 Å
Translation7.4 Å47.68 Å

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RXW

3rxw


Resolution: 1.787→47.677 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2052 1983 1.83 %
Rwork0.1704 --
obs0.171 108182 77.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.22 Å2 / Biso mean: 23.3258 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: final / Resolution: 1.787→47.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7839 0 190 811 8840
Biso mean--34.03 31.5 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118165
X-RAY DIFFRACTIONf_angle_d1.15211064
X-RAY DIFFRACTIONf_chiral_restr0.0641244
X-RAY DIFFRACTIONf_plane_restr0.0071437
X-RAY DIFFRACTIONf_dihedral_angle_d16.1424824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7871-1.83180.275370.2734664735
1.8318-1.88140.3154290.26911469149815
1.8814-1.93670.3736530.25722861291429
1.9367-1.99920.31781010.25165512561356
1.9992-2.07070.28761410.23378021816281
2.0707-2.15360.25421810.20759509969097
2.1536-2.25160.23821840.18659650983499
2.2516-2.37030.2361820.17589720990299
2.3703-2.51880.19821800.16629669984999
2.5188-2.71330.17941790.15929760993999
2.7133-2.98630.23761870.16759803999099
2.9863-3.41830.1861830.16919764994799
3.4183-4.30630.16871920.142992110113100
4.3063-47.69420.18271840.1602100741025899

+
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