Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

2DW7

Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0016829molecular_functionlyase activity
A0046872molecular_functionmetal ion binding
A0047808molecular_functionD(-)-tartrate dehydratase activity
A0051260biological_processprotein homooligomerization
B0000287molecular_functionmagnesium ion binding
B0016829molecular_functionlyase activity
B0046872molecular_functionmetal ion binding
B0047808molecular_functionD(-)-tartrate dehydratase activity
B0051260biological_processprotein homooligomerization
C0000287molecular_functionmagnesium ion binding
C0016829molecular_functionlyase activity
C0046872molecular_functionmetal ion binding
C0047808molecular_functionD(-)-tartrate dehydratase activity
C0051260biological_processprotein homooligomerization
D0000287molecular_functionmagnesium ion binding
D0016829molecular_functionlyase activity
D0046872molecular_functionmetal ion binding
D0047808molecular_functionD(-)-tartrate dehydratase activity
D0051260biological_processprotein homooligomerization
E0000287molecular_functionmagnesium ion binding
E0016829molecular_functionlyase activity
E0046872molecular_functionmetal ion binding
E0047808molecular_functionD(-)-tartrate dehydratase activity
E0051260biological_processprotein homooligomerization
F0000287molecular_functionmagnesium ion binding
F0016829molecular_functionlyase activity
F0046872molecular_functionmetal ion binding
F0047808molecular_functionD(-)-tartrate dehydratase activity
F0051260biological_processprotein homooligomerization
G0000287molecular_functionmagnesium ion binding
G0016829molecular_functionlyase activity
G0046872molecular_functionmetal ion binding
G0047808molecular_functionD(-)-tartrate dehydratase activity
G0051260biological_processprotein homooligomerization
H0000287molecular_functionmagnesium ion binding
H0016829molecular_functionlyase activity
H0046872molecular_functionmetal ion binding
H0047808molecular_functionD(-)-tartrate dehydratase activity
H0051260biological_processprotein homooligomerization
I0000287molecular_functionmagnesium ion binding
I0016829molecular_functionlyase activity
I0046872molecular_functionmetal ion binding
I0047808molecular_functionD(-)-tartrate dehydratase activity
I0051260biological_processprotein homooligomerization
J0000287molecular_functionmagnesium ion binding
J0016829molecular_functionlyase activity
J0046872molecular_functionmetal ion binding
J0047808molecular_functionD(-)-tartrate dehydratase activity
J0051260biological_processprotein homooligomerization
K0000287molecular_functionmagnesium ion binding
K0016829molecular_functionlyase activity
K0046872molecular_functionmetal ion binding
K0047808molecular_functionD(-)-tartrate dehydratase activity
K0051260biological_processprotein homooligomerization
L0000287molecular_functionmagnesium ion binding
L0016829molecular_functionlyase activity
L0046872molecular_functionmetal ion binding
L0047808molecular_functionD(-)-tartrate dehydratase activity
L0051260biological_processprotein homooligomerization
M0000287molecular_functionmagnesium ion binding
M0016829molecular_functionlyase activity
M0046872molecular_functionmetal ion binding
M0047808molecular_functionD(-)-tartrate dehydratase activity
M0051260biological_processprotein homooligomerization
N0000287molecular_functionmagnesium ion binding
N0016829molecular_functionlyase activity
N0046872molecular_functionmetal ion binding
N0047808molecular_functionD(-)-tartrate dehydratase activity
N0051260biological_processprotein homooligomerization
O0000287molecular_functionmagnesium ion binding
O0016829molecular_functionlyase activity
O0046872molecular_functionmetal ion binding
O0047808molecular_functionD(-)-tartrate dehydratase activity
O0051260biological_processprotein homooligomerization
P0000287molecular_functionmagnesium ion binding
P0016829molecular_functionlyase activity
P0046872molecular_functionmetal ion binding
P0047808molecular_functionD(-)-tartrate dehydratase activity
P0051260biological_processprotein homooligomerization
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 2001
ChainResidue
AASP213
AGLU239
AGLU240
AGLU265
ASRT1001

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 2002
ChainResidue
BSRT1002
BASP213
BGLU239
BGLU240
BGLU265

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 2003
ChainResidue
CASP213
CASN215
CGLU239
CGLU240
CGLU265
CSRT1003

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG D 2004
ChainResidue
DASP213
DGLU239
DGLU265
DSRT1004

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG E 2005
ChainResidue
EASP213
EGLU239
EGLU240
EGLU265
ESRT1005

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG F 2006
ChainResidue
FASP213
FASN215
FGLU239
FGLU240
FGLU265
FSRT1006

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG G 2007
ChainResidue
GASP213
GASN215
GGLU239
GGLU240
GGLU265
GSRT1007

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG H 2008
ChainResidue
HASP213
HASN215
HGLU239
HGLU240
HGLU265
HSRT1008

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG I 2009
ChainResidue
IASP213
IASN215
IGLU239
IGLU240
IGLU265
ISRT1009

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG J 2010
ChainResidue
JASP213
JGLU239
JGLU240
JGLU265
JSRT1010

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG K 2011
ChainResidue
KASP213
KASN215
KGLU239
KGLU240
KGLU265
KSRT1011

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG L 2012
ChainResidue
LASP213
LASN215
LGLU239
LGLU240
LGLU265
LSRT1012

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG M 2013
ChainResidue
MASP213
MGLU239
MGLU240
MGLU265
MSRT1013

site_idBC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG N 2014
ChainResidue
NASP213
NGLU239
NGLU265
NSRT1014

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG O 2015
ChainResidue
OASP213
OGLU239
OGLU265
OSRT1015

site_idBC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG P 2016
ChainResidue
PASP213
PASN215
PGLU239
PGLU240
PGLU265
PSRT1016

site_idBC8
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT A 1001
ChainResidue
BLYS102
AASN21
APHE26
AASN55
ATYR156
ALYS182
ALYS184
AASP213
AASN215
AGLU239
AGLU265
AHIS322
AGLU341
ATYR343
AMG2001

site_idBC9
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT B 1002
ChainResidue
ALYS102
BASN21
BPHE26
BASN55
BTYR156
BLYS182
BLYS184
BASP213
BASN215
BGLU239
BGLU265
BHIS322
BGLU341
BTYR343
BMG2002

site_idCC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT C 1003
ChainResidue
CASN21
CPHE26
CASN55
CTYR156
CLYS182
CLYS184
CASP213
CASN215
CGLU239
CGLU265
CHIS322
CGLU341
CTYR343
CMG2003
DLYS102

site_idCC2
Number of Residues16
DetailsBINDING SITE FOR RESIDUE SRT D 1004
ChainResidue
CLYS102
DASN21
DPHE26
DASN55
DTYR156
DLYS182
DLYS184
DASP213
DASN215
DGLU239
DGLU265
DHIS322
DGLU341
DTYR343
DMG2004
DHOH2022

site_idCC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT E 1005
ChainResidue
EASN21
EPHE26
EASN55
ETYR156
ELYS182
ELYS184
EASP213
EASN215
EGLU239
EGLU265
EHIS322
EGLU341
ETYR343
EMG2005
FLYS102

site_idCC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT F 1006
ChainResidue
ELYS102
FASN21
FPHE26
FASN55
FTYR156
FLYS182
FLYS184
FASP213
FASN215
FGLU239
FGLU265
FHIS322
FGLU341
FTYR343
FMG2006

site_idCC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT G 1007
ChainResidue
GASN21
GPHE26
GASN55
GTYR156
GLYS182
GLYS184
GASP213
GASN215
GGLU239
GGLU265
GHIS322
GGLU341
GTYR343
GMG2007
HLYS102

site_idCC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT H 1008
ChainResidue
GLYS102
HASN21
HPHE26
HASN55
HTYR156
HLYS182
HLYS184
HASP213
HASN215
HGLU239
HGLU265
HHIS322
HGLU341
HTYR343
HMG2008

site_idCC7
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT I 1009
ChainResidue
IASN21
IPHE26
IASN55
ITYR156
ILYS182
ILYS184
IASP213
IASN215
IGLU239
IGLU265
IHIS322
IGLU341
ITYR343
IMG2009
JLYS102

site_idCC8
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT J 1010
ChainResidue
ILYS102
JASN21
JPHE26
JASN55
JTYR156
JLYS182
JLYS184
JASP213
JASN215
JGLU239
JGLU265
JHIS322
JGLU341
JTYR343
JMG2010

site_idCC9
Number of Residues16
DetailsBINDING SITE FOR RESIDUE SRT K 1011
ChainResidue
KASN21
KPHE26
KASN55
KTYR156
KLYS182
KLYS184
KASP213
KASN215
KGLU239
KGLU265
KHIS322
KGLU341
KTYR343
KMG2011
KHOH2036
LLYS102

site_idDC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT L 1012
ChainResidue
KLYS102
LASN21
LPHE26
LASN55
LTYR156
LLYS182
LLYS184
LASP213
LASN215
LGLU239
LGLU265
LHIS322
LGLU341
LTYR343
LMG2012

site_idDC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT M 1013
ChainResidue
MASN21
MPHE26
MASN55
MTYR156
MLYS182
MLYS184
MASP213
MASN215
MGLU239
MGLU265
MHIS322
MGLU341
MTYR343
MMG2013
NLYS102

site_idDC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT N 1014
ChainResidue
MLYS102
NASN21
NPHE26
NASN55
NTYR156
NLYS182
NLYS184
NASP213
NASN215
NGLU239
NGLU265
NHIS322
NGLU341
NTYR343
NMG2014

site_idDC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT O 1015
ChainResidue
OASN21
OPHE26
OASN55
OTYR156
OLYS182
OLYS184
OASP213
OASN215
OGLU239
OGLU265
OHIS322
OGLU341
OTYR343
OMG2015
PLYS102

site_idDC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SRT P 1016
ChainResidue
OLYS102
PASN21
PPHE26
PASN55
PTYR156
PLYS182
PLYS184
PASP213
PASN215
PGLU239
PGLU265
PHIS322
PGLU341
PTYR343
PMG2016

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsACT_SITE: acceptor => ECO:0000269|PubMed:17144653
ChainResidueDetails
ALYS184
BLYS184
CLYS184
DLYS184
ELYS184
FLYS184
GLYS184
HLYS184
ILYS184
JLYS184
KLYS184
LLYS184
MLYS184
NLYS184
OLYS184
PLYS184

site_idSWS_FT_FI2
Number of Residues16
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:17144653
ChainResidueDetails
AHIS322
BHIS322
CHIS322
DHIS322
EHIS322
FHIS322
GHIS322
HHIS322
IHIS322
JHIS322
KHIS322
LHIS322
MHIS322
NHIS322
OHIS322
PHIS322

site_idSWS_FT_FI3
Number of Residues144
DetailsBINDING:
ChainResidueDetails
FTYR156
FLYS182
FGLU239
FGLU265
FHIS322
FGLU341
GASN21
GASN55
GLYS102
GTYR156
GLYS182
GGLU239
GGLU265
GHIS322
GGLU341
HASN21
HASN55
HLYS102
HTYR156
HLYS182
HGLU239
HGLU265
HHIS322
HGLU341
IASN21
IASN55
ILYS102
ITYR156
ILYS182
IGLU239
IGLU265
IHIS322
IGLU341
JASN21
JASN55
JLYS102
JTYR156
JLYS182
JGLU239
JGLU265
JHIS322
JGLU341
KASN21
KASN55
KLYS102
KTYR156
KLYS182
KGLU239
KGLU265
KHIS322
KGLU341
LASN21
LASN55
LLYS102
LTYR156
LLYS182
LGLU239
LGLU265
LHIS322
LGLU341
MASN21
MASN55
MLYS102
MTYR156
MLYS182
MGLU239
MGLU265
MHIS322
MGLU341
NASN21
NASN55
NLYS102
NTYR156
NLYS182
NGLU239
NGLU265
NHIS322
NGLU341
OASN21
OASN55
OLYS102
OTYR156
OLYS182
OGLU239
OGLU265
OHIS322
OGLU341
PASN21
PASN55
PLYS102
PTYR156
PLYS182
PGLU239
PGLU265
PHIS322
PGLU341
AASN21
AASN55
ALYS102
ATYR156
ALYS182
AGLU239
AGLU265
AHIS322
AGLU341
BASN21
BASN55
BLYS102
BTYR156
BLYS182
BGLU239
BGLU265
BHIS322
BGLU341
CASN21
CASN55
CLYS102
CTYR156
CLYS182
CGLU239
CGLU265
CHIS322
CGLU341
DASN21
DASN55
DLYS102
DTYR156
DLYS182
DGLU239
DGLU265
DHIS322
DGLU341
EASN21
EASN55
ELYS102
ETYR156
ELYS182
EGLU239
EGLU265
EHIS322
EGLU341
FASN21
FASN55
FLYS102

site_idSWS_FT_FI4
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:17144653
ChainResidueDetails
AASP213
BASP213
CASP213
DASP213
EASP213
FASP213
GASP213
HASP213
IASP213
JASP213
KASP213
LASP213
MASP213
NASP213
OASP213
PASP213

site_idSWS_FT_FI5
Number of Residues48
DetailsSITE: Transition state stabilizer
ChainResidueDetails
AASN55
ALYS182
AGLU341
BASN55
BLYS182
BGLU341
CASN55
CLYS182
CGLU341
DASN55
DLYS182
DGLU341
EASN55
ELYS182
EGLU341
FASN55
FLYS182
FGLU341
GASN55
GLYS182
GGLU341
HASN55
HLYS182
HGLU341
IASN55
ILYS182
IGLU341
JASN55
JLYS182
JGLU341
KASN55
KLYS182
KGLU341
LASN55
LLYS182
LGLU341
MASN55
MLYS182
MGLU341
NASN55
NLYS182
NGLU341
OASN55
OLYS182
OGLU341
PASN55
PLYS182
PGLU341

site_idSWS_FT_FI6
Number of Residues16
DetailsSITE: Increases basicity of active site His
ChainResidueDetails
AASP292
BASP292
CASP292
DASP292
EASP292
FASP292
GASP292
HASP292
IASP292
JASP292
KASP292
LASP292
MASP292
NASP292
OASP292
PASP292

Catalytic Information from CSA
site_idMCSA1
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
AASN55electrostatic stabiliser
ALYS182electrostatic stabiliser
ALYS184proton acceptor, proton donor
AASP213metal ligand
AGLU239metal ligand
AGLU265metal ligand
AASP292electrostatic stabiliser, increase basicity, modifies pKa
AHIS322proton acceptor, proton donor
AGLU341electrostatic stabiliser

site_idMCSA2
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
BASN55electrostatic stabiliser
BLYS182electrostatic stabiliser
BLYS184proton acceptor, proton donor
BASP213metal ligand
BGLU239metal ligand
BGLU265metal ligand
BASP292electrostatic stabiliser, increase basicity, modifies pKa
BHIS322proton acceptor, proton donor
BGLU341electrostatic stabiliser

site_idMCSA3
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
CASN55electrostatic stabiliser
CLYS182electrostatic stabiliser
CLYS184proton acceptor, proton donor
CASP213metal ligand
CGLU239metal ligand
CGLU265metal ligand
CASP292electrostatic stabiliser, increase basicity, modifies pKa
CHIS322proton acceptor, proton donor
CGLU341electrostatic stabiliser

site_idMCSA4
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
DASN55electrostatic stabiliser
DLYS182electrostatic stabiliser
DLYS184proton acceptor, proton donor
DASP213metal ligand
DGLU239metal ligand
DGLU265metal ligand
DASP292electrostatic stabiliser, increase basicity, modifies pKa
DHIS322proton acceptor, proton donor
DGLU341electrostatic stabiliser

site_idMCSA5
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
EASN55electrostatic stabiliser
ELYS182electrostatic stabiliser
ELYS184proton acceptor, proton donor
EASP213metal ligand
EGLU239metal ligand
EGLU265metal ligand
EASP292electrostatic stabiliser, increase basicity, modifies pKa
EHIS322proton acceptor, proton donor
EGLU341electrostatic stabiliser

site_idMCSA6
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
FASN55electrostatic stabiliser
FLYS182electrostatic stabiliser
FLYS184proton acceptor, proton donor
FASP213metal ligand
FGLU239metal ligand
FGLU265metal ligand
FASP292electrostatic stabiliser, increase basicity, modifies pKa
FHIS322proton acceptor, proton donor
FGLU341electrostatic stabiliser

site_idMCSA7
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
GASN55electrostatic stabiliser
GLYS182electrostatic stabiliser
GLYS184proton acceptor, proton donor
GASP213metal ligand
GGLU239metal ligand
GGLU265metal ligand
GASP292electrostatic stabiliser, increase basicity, modifies pKa
GHIS322proton acceptor, proton donor
GGLU341electrostatic stabiliser

site_idMCSA8
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
HASN55electrostatic stabiliser
HLYS182electrostatic stabiliser
HLYS184proton acceptor, proton donor
HASP213metal ligand
HGLU239metal ligand
HGLU265metal ligand
HASP292electrostatic stabiliser, increase basicity, modifies pKa
HHIS322proton acceptor, proton donor
HGLU341electrostatic stabiliser

site_idMCSA9
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
IASN55electrostatic stabiliser
ILYS182electrostatic stabiliser
ILYS184proton acceptor, proton donor
IASP213metal ligand
IGLU239metal ligand
IGLU265metal ligand
IASP292electrostatic stabiliser, increase basicity, modifies pKa
IHIS322proton acceptor, proton donor
IGLU341electrostatic stabiliser

site_idMCSA10
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
JASN55electrostatic stabiliser
JLYS182electrostatic stabiliser
JLYS184proton acceptor, proton donor
JASP213metal ligand
JGLU239metal ligand
JGLU265metal ligand
JASP292electrostatic stabiliser, increase basicity, modifies pKa
JHIS322proton acceptor, proton donor
JGLU341electrostatic stabiliser

site_idMCSA11
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
KASN55electrostatic stabiliser
KLYS182electrostatic stabiliser
KLYS184proton acceptor, proton donor
KASP213metal ligand
KGLU239metal ligand
KGLU265metal ligand
KASP292electrostatic stabiliser, increase basicity, modifies pKa
KHIS322proton acceptor, proton donor
KGLU341electrostatic stabiliser

site_idMCSA12
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
LASN55electrostatic stabiliser
LLYS182electrostatic stabiliser
LLYS184proton acceptor, proton donor
LASP213metal ligand
LGLU239metal ligand
LGLU265metal ligand
LASP292electrostatic stabiliser, increase basicity, modifies pKa
LHIS322proton acceptor, proton donor
LGLU341electrostatic stabiliser

site_idMCSA13
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
MASN55electrostatic stabiliser
MLYS182electrostatic stabiliser
MLYS184proton acceptor, proton donor
MASP213metal ligand
MGLU239metal ligand
MGLU265metal ligand
MASP292electrostatic stabiliser, increase basicity, modifies pKa
MHIS322proton acceptor, proton donor
MGLU341electrostatic stabiliser

site_idMCSA14
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
NASN55electrostatic stabiliser
NLYS182electrostatic stabiliser
NLYS184proton acceptor, proton donor
NASP213metal ligand
NGLU239metal ligand
NGLU265metal ligand
NASP292electrostatic stabiliser, increase basicity, modifies pKa
NHIS322proton acceptor, proton donor
NGLU341electrostatic stabiliser

site_idMCSA15
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
OASN55electrostatic stabiliser
OLYS182electrostatic stabiliser
OLYS184proton acceptor, proton donor
OASP213metal ligand
OGLU239metal ligand
OGLU265metal ligand
OASP292electrostatic stabiliser, increase basicity, modifies pKa
OHIS322proton acceptor, proton donor
OGLU341electrostatic stabiliser

site_idMCSA16
Number of Residues9
DetailsM-CSA 463
ChainResidueDetails
PASN55electrostatic stabiliser
PLYS182electrostatic stabiliser
PLYS184proton acceptor, proton donor
PASP213metal ligand
PGLU239metal ligand
PGLU265metal ligand
PASP292electrostatic stabiliser, increase basicity, modifies pKa
PHIS322proton acceptor, proton donor
PGLU341electrostatic stabiliser

219869

PDB entries from 2024-05-15

PDB statisticsPDBj update infoContact PDBjnumon