5A1A

2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor

> Summary

Summary for 5A1A

EMDB informationEMD-2984
DescriptorBETA-GALACTOSIDASE (E.C.3.2.1.23)
Functional Keywordshydrolase, near-atomic, near-atomic resolution cryo-electron microscopy, single- particle cryo-em, protein complexes, petg
Biological sourceESCHERICHIA COLI K-12
Total number of polymer chains4
Total molecular weight467064.52
Authors
Bartesaghi, A.,Merk, A.,Banerjee, S.,Matthies, D.,Wu, X.,Milne, J.,Subramaniam, S. (deposition date: 2015-04-29, release date: 2015-05-06, Last modification date: 2015-06-24)
Primary citation
Bartesaghi, A.,Merk, A.,Banerjee, S.,Matthies, D.,Wu, X.,Milne, J.,Subramaniam, S.
2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with a Cell-Permeant Inhibitor
Science, 348:1147-, 2015
PubMed: 25953817
DOI: 10.1126/SCIENCE.AAB1576
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY (2.2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers140.6%0.3%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 5a1a
no rotation
Molmil generated image of 5a1a
rotated about x axis by 90°
Molmil generated image of 5a1a
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, DBETA-GALACTOSIDASEpolymer1022116371.24
UniProt (P00722)
Pfam (PF00703)
Pfam (PF02836)
Pfam (PF02837)
Pfam (PF02929)
Pfam (PF16353)
ESCHERICHIA COLI K-12BETA-GAL, LACTASE
SUGAR (2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE)non-polymer300.44
MAGNESIUM IONnon-polymer24.38
SODIUM IONnon-polymer23.08
waterwater18.0776

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight465484.7
Non-Polymers*Number of molecules20
Total molecular weight1579.8
All*Total molecular weight467064.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY (2.2 Å)

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits - 2.20
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0009341cellular_componentbeta-galactosidase complex
A0043231cellular_componentintracellular membrane-bounded organelle
A0031420molecular_functionalkali metal ion binding
A0004565molecular_functionbeta-galactosidase activity
A0030246molecular_functioncarbohydrate binding
A0000287molecular_functionmagnesium ion binding
A0005990biological_processlactose catabolic process
B0009341cellular_componentbeta-galactosidase complex
B0043231cellular_componentintracellular membrane-bounded organelle
B0031420molecular_functionalkali metal ion binding
B0004565molecular_functionbeta-galactosidase activity
B0030246molecular_functioncarbohydrate binding
B0000287molecular_functionmagnesium ion binding
B0005990biological_processlactose catabolic process
C0009341cellular_componentbeta-galactosidase complex
C0043231cellular_componentintracellular membrane-bounded organelle
C0031420molecular_functionalkali metal ion binding
C0004565molecular_functionbeta-galactosidase activity
C0030246molecular_functioncarbohydrate binding
C0000287molecular_functionmagnesium ion binding
C0005990biological_processlactose catabolic process
D0009341cellular_componentbeta-galactosidase complex
D0043231cellular_componentintracellular membrane-bounded organelle
D0031420molecular_functionalkali metal ion binding
D0004565molecular_functionbeta-galactosidase activity
D0030246molecular_functioncarbohydrate binding
D0000287molecular_functionmagnesium ion binding
D0005990biological_processlactose catabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC112BINDING SITE FOR RESIDUE PTQ A 2001
ChainResidue
AASN102
AASP201
AMET502
ATYR503
AGLU537
AHIS540
AASP598
APHE601
ATRP999
ANA4001
AHOH5037
AHOH5079

AC26BINDING SITE FOR RESIDUE MG A 3001
ChainResidue
AGLU416
AHIS418
AGLU461
AHOH5036
AHOH5037
AHOH5078

AC36BINDING SITE FOR RESIDUE MG A 3002
ChainResidue
AASP15
AASN18
AVAL21
ATYR161
AGLN163
AASP193

AC45BINDING SITE FOR RESIDUE NA A 4001
ChainResidue
AASP201
APHE601
AASN604
APTQ2001
AHOH5013

AC55BINDING SITE FOR RESIDUE NA A 4002
ChainResidue
APHE556
ATYR559
APRO560
ALEU562
AHOH5082

AC612BINDING SITE FOR RESIDUE PTQ B 2001
ChainResidue
BASN102
BASP201
BMET502
BTYR503
BGLU537
BHIS540
BASP598
BPHE601
BTRP999
BNA4001
BHOH5037
BHOH5079

AC76BINDING SITE FOR RESIDUE MG B 3001
ChainResidue
BGLU416
BHIS418
BGLU461
BHOH5036
BHOH5037
BHOH5078

AC86BINDING SITE FOR RESIDUE MG B 3002
ChainResidue
BASP15
BASN18
BVAL21
BTYR161
BGLN163
BASP193

AC95BINDING SITE FOR RESIDUE NA B 4001
ChainResidue
BASP201
BPHE601
BASN604
BPTQ2001
BHOH5013

BC15BINDING SITE FOR RESIDUE NA B 4002
ChainResidue
BPHE556
BTYR559
BPRO560
BLEU562
BHOH5082

BC212BINDING SITE FOR RESIDUE PTQ C 2001
ChainResidue
CASN102
CASP201
CMET502
CTYR503
CGLU537
CHIS540
CASP598
CPHE601
CTRP999
CNA4001
CHOH5037
CHOH5079

BC36BINDING SITE FOR RESIDUE MG C 3001
ChainResidue
CGLU416
CHIS418
CGLU461
CHOH5036
CHOH5037
CHOH5078

BC46BINDING SITE FOR RESIDUE MG C 3002
ChainResidue
CASP15
CASN18
CVAL21
CTYR161
CGLN163
CASP193

BC55BINDING SITE FOR RESIDUE NA C 4001
ChainResidue
CASP201
CPHE601
CASN604
CPTQ2001
CHOH5013

BC65BINDING SITE FOR RESIDUE NA C 4002
ChainResidue
CPHE556
CTYR559
CPRO560
CLEU562
CHOH5082

BC712BINDING SITE FOR RESIDUE PTQ D 2001
ChainResidue
DASN102
DASP201
DMET502
DTYR503
DGLU537
DHIS540
DASP598
DPHE601
DTRP999
DNA4001
DHOH5037
DHOH5079

BC86BINDING SITE FOR RESIDUE MG D 3001
ChainResidue
DGLU416
DHIS418
DGLU461
DHOH5036
DHOH5037
DHOH5078

BC96BINDING SITE FOR RESIDUE MG D 3002
ChainResidue
DASP15
DASN18
DVAL21
DTYR161
DGLN163
DASP193

CC15BINDING SITE FOR RESIDUE NA D 4001
ChainResidue
DASP201
DPHE601
DASN604
DPTQ2001
DHOH5013

CC25BINDING SITE FOR RESIDUE NA D 4002
ChainResidue
DPHE556
DTYR559
DPRO560
DLEU562
DHOH5082

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
PTQ_5a1a_A_2001162-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE binding site
ChainResidueligand
ATYR100PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AASN102-VAL103PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AASP201PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AHIS418PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AGLU461PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AMET502-TYR503PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AGLU537PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AHIS540PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
ATRP568PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AASP598PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
APHE601PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AASN604PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
AVAL795PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
ATRP999PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE

PTQ_5a1a_B_2001162-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE binding site
ChainResidueligand
BTYR100PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BASN102-VAL103PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BASP201PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BHIS418PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BGLU461PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BMET502-TYR503PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BGLU537PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BHIS540PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BTRP568PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BASP598PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BPHE601PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BASN604PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BVAL795PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
BTRP999PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE

PTQ_5a1a_C_2001162-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE binding site
ChainResidueligand
CTYR100PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CASN102-VAL103PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CASP201PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CHIS418PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CGLU461PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CMET502-TYR503PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CGLU537PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CHIS540PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CTRP568PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CASP598PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CPHE601PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CASN604PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CVAL795PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
CTRP999PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE

PTQ_5a1a_D_2001162-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE binding site
ChainResidueligand
DTYR100PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DASN102-VAL103PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DASP201PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DHIS418PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DGLU461PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DMET502-TYR503PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DGLU537PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DHIS540PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DTRP568PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DASP598PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DPHE601PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DASN604PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DVAL795PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE
DTRP999PTQ: 2-PHENYLETHYL 1-THIO-BETA-D-GALACTOPYRANOSIDE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nucleophile. {ECO:0000269|PubMed:1350782}.
ChainResidueDetails
AGLU536

SWS_FT_FI21Proton donor. {ECO:0000269|PubMed:6420154}.
ChainResidueDetails
AGLU460

SWS_FT_FI75Substrate.
ChainResidueDetails
AASN101
AASP200
AGLU460
AASN603
ATRP998

SWS_FT_FI101Nucleophile. {ECO:0000269|PubMed:1350782}.
ChainResidueDetails
BGLU536

SWS_FT_FI111Proton donor. {ECO:0000269|PubMed:6420154}.
ChainResidueDetails
BGLU460

SWS_FT_FI165Substrate.
ChainResidueDetails
BASN101
BASP200
BGLU460
BASN603
BTRP998

SWS_FT_FI191Nucleophile. {ECO:0000269|PubMed:1350782}.
ChainResidueDetails
CGLU536

SWS_FT_FI201Proton donor. {ECO:0000269|PubMed:6420154}.
ChainResidueDetails
CGLU460

SWS_FT_FI255Substrate.
ChainResidueDetails
CASN101
CASP200
CGLU460
CASN603
CTRP998

SWS_FT_FI281Nucleophile. {ECO:0000269|PubMed:1350782}.
ChainResidueDetails
DGLU536

SWS_FT_FI291Proton donor. {ECO:0000269|PubMed:6420154}.
ChainResidueDetails
DGLU460

SWS_FT_FI345Substrate.
ChainResidueDetails
DASN101
DASP200
DGLU460
DASN603
DTRP998

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

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