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2BVC

Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0000287molecular_functionmagnesium ion binding
A0001968molecular_functionfibronectin binding
A0003824molecular_functioncatalytic activity
A0004356molecular_functionglutamine synthetase activity
A0005524molecular_functionATP binding
A0005576cellular_componentextracellular region
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006542biological_processglutamine biosynthetic process
A0009274cellular_componentpeptidoglycan-based cell wall
A0010756biological_processpositive regulation of plasminogen activation
A0016020cellular_componentmembrane
A0016874molecular_functionligase activity
A0019740biological_processnitrogen utilization
A0035375molecular_functionzymogen binding
A0046872molecular_functionmetal ion binding
A0051260biological_processprotein homooligomerization
B0000166molecular_functionnucleotide binding
B0000287molecular_functionmagnesium ion binding
B0001968molecular_functionfibronectin binding
B0003824molecular_functioncatalytic activity
B0004356molecular_functionglutamine synthetase activity
B0005524molecular_functionATP binding
B0005576cellular_componentextracellular region
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005886cellular_componentplasma membrane
B0006542biological_processglutamine biosynthetic process
B0009274cellular_componentpeptidoglycan-based cell wall
B0010756biological_processpositive regulation of plasminogen activation
B0016020cellular_componentmembrane
B0016874molecular_functionligase activity
B0019740biological_processnitrogen utilization
B0035375molecular_functionzymogen binding
B0046872molecular_functionmetal ion binding
B0051260biological_processprotein homooligomerization
C0000166molecular_functionnucleotide binding
C0000287molecular_functionmagnesium ion binding
C0001968molecular_functionfibronectin binding
C0003824molecular_functioncatalytic activity
C0004356molecular_functionglutamine synthetase activity
C0005524molecular_functionATP binding
C0005576cellular_componentextracellular region
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006542biological_processglutamine biosynthetic process
C0009274cellular_componentpeptidoglycan-based cell wall
C0010756biological_processpositive regulation of plasminogen activation
C0016020cellular_componentmembrane
C0016874molecular_functionligase activity
C0019740biological_processnitrogen utilization
C0035375molecular_functionzymogen binding
C0046872molecular_functionmetal ion binding
C0051260biological_processprotein homooligomerization
D0000166molecular_functionnucleotide binding
D0000287molecular_functionmagnesium ion binding
D0001968molecular_functionfibronectin binding
D0003824molecular_functioncatalytic activity
D0004356molecular_functionglutamine synthetase activity
D0005524molecular_functionATP binding
D0005576cellular_componentextracellular region
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0005886cellular_componentplasma membrane
D0006542biological_processglutamine biosynthetic process
D0009274cellular_componentpeptidoglycan-based cell wall
D0010756biological_processpositive regulation of plasminogen activation
D0016020cellular_componentmembrane
D0016874molecular_functionligase activity
D0019740biological_processnitrogen utilization
D0035375molecular_functionzymogen binding
D0046872molecular_functionmetal ion binding
D0051260biological_processprotein homooligomerization
E0000166molecular_functionnucleotide binding
E0000287molecular_functionmagnesium ion binding
E0001968molecular_functionfibronectin binding
E0003824molecular_functioncatalytic activity
E0004356molecular_functionglutamine synthetase activity
E0005524molecular_functionATP binding
E0005576cellular_componentextracellular region
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0005886cellular_componentplasma membrane
E0006542biological_processglutamine biosynthetic process
E0009274cellular_componentpeptidoglycan-based cell wall
E0010756biological_processpositive regulation of plasminogen activation
E0016020cellular_componentmembrane
E0016874molecular_functionligase activity
E0019740biological_processnitrogen utilization
E0035375molecular_functionzymogen binding
E0046872molecular_functionmetal ion binding
E0051260biological_processprotein homooligomerization
F0000166molecular_functionnucleotide binding
F0000287molecular_functionmagnesium ion binding
F0001968molecular_functionfibronectin binding
F0003824molecular_functioncatalytic activity
F0004356molecular_functionglutamine synthetase activity
F0005524molecular_functionATP binding
F0005576cellular_componentextracellular region
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0005886cellular_componentplasma membrane
F0006542biological_processglutamine biosynthetic process
F0009274cellular_componentpeptidoglycan-based cell wall
F0010756biological_processpositive regulation of plasminogen activation
F0016020cellular_componentmembrane
F0016874molecular_functionligase activity
F0019740biological_processnitrogen utilization
F0035375molecular_functionzymogen binding
F0046872molecular_functionmetal ion binding
F0051260biological_processprotein homooligomerization
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 502
ChainResidue
AGLU135
AGLU219
AGLU227
AP3S500
AHOH2028

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 503
ChainResidue
AADP501
AGLU133
AHIS276
AGLU366
AP3S500

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 504
ChainResidue
AGLU133
AGLU227
AP3S500
AADP501
AHOH2067

site_idAC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL A 505
ChainResidue
FSER424

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 502
ChainResidue
BGLU135
BGLU219
BGLU227
BP3S500
BHOH2091

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 503
ChainResidue
BGLU133
BHIS276
BGLU366
BARG368
BP3S500
BADP501

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 504
ChainResidue
BGLU133
BGLU227
BP3S500
BADP501
BHOH2057

site_idAC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL B 505
ChainResidue
ESER424

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C 502
ChainResidue
CGLU135
CGLU219
CGLU227
CP3S500
CHOH2087

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 503
ChainResidue
CGLU133
CHIS276
CGLU366
CARG368
CP3S500
CADP501

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C 504
ChainResidue
CGLU133
CGLU227
CP3S500
CADP501
CHOH2053

site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE CL C 505
ChainResidue
ASER424
AHOH2109

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D 502
ChainResidue
DGLU135
DGLU219
DGLU227
DP3S500
DHOH2063

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG D 503
ChainResidue
DGLU133
DHIS276
DGLU366
DARG368
DP3S500
DADP501

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D 504
ChainResidue
DGLU133
DGLU227
DP3S500
DADP501
DHOH2059

site_idBC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL D 505
ChainResidue
BSER424

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG E 502
ChainResidue
EGLU135
EGLU219
EGLU227
EP3S500
EMG504
EHOH2073

site_idBC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG E 503
ChainResidue
EGLU133
EHIS276
EGLU366
EP3S500
EADP501

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG E 504
ChainResidue
EGLU133
EGLU227
EP3S500
EADP501
EMG502
EHOH2074

site_idCC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL E 505
ChainResidue
CSER424

site_idCC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG F 502
ChainResidue
FGLU135
FGLU219
FGLU227
FP3S500
FMG504
FHOH2027

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG F 503
ChainResidue
FGLU133
FHIS276
FGLU366
FP3S500
FADP501

site_idCC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG F 504
ChainResidue
FP3S500
FADP501
FMG502
FHOH2105
FGLU133
FGLU227

site_idCC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL F 505
ChainResidue
DSER424

site_idCC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE P3S A 500
ChainResidue
AGLU133
AGLU135
AGLU219
AGLU227
AGLY272
AHIS276
AARG329
ATYR334
AGLU335
AARG347
AGLU366
AARG368
AADP501
AMG502
AMG503
AMG504
AHOH2028
AHOH2047
AHOH2067
AHOH2116
AHOH2117
FASP54

site_idCC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE ADP A 501
ChainResidue
AGLU133
AGLU214
ALYS215
AGLU227
AASN229
ATYR230
AGLN231
APHE232
AHIS278
ASER280
AARG347
AARG352
ALYS361
AARG364
AGLU366
AP3S500
AMG503
AMG504
AHOH2025
AHOH2067
AHOH2094
AHOH2118
AHOH2119

site_idCC9
Number of Residues20
DetailsBINDING SITE FOR RESIDUE P3S B 500
ChainResidue
AASP54
BGLU133
BGLU135
BGLU219
BGLU227
BGLY272
BHIS276
BARG329
BGLU335
BARG347
BGLU366
BARG368
BADP501
BMG502
BMG503
BMG504
BHOH2038
BHOH2076
BHOH2091
BHOH2092

site_idDC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE ADP B 501
ChainResidue
BGLU133
BGLU214
BLYS215
BGLU227
BASN229
BTYR230
BGLN231
BPHE232
BHIS278
BSER280
BARG347
BARG352
BLYS361
BARG364
BGLU366
BP3S500
BMG503
BMG504
BHOH2014
BHOH2055
BHOH2057

site_idDC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE P3S C 500
ChainResidue
BASP54
CGLU133
CGLU135
CGLU219
CGLU227
CGLY272
CHIS276
CARG329
CGLU335
CARG347
CGLU366
CARG368
CADP501
CMG502
CMG503
CMG504
CHOH2038
CHOH2053
CHOH2069
CHOH2086
CHOH2087

site_idDC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE ADP C 501
ChainResidue
CGLU133
CGLU214
CLYS215
CGLU227
CASN229
CTYR230
CGLN231
CPHE232
CHIS278
CSER280
CARG347
CARG352
CLYS361
CARG364
CGLU366
CP3S500
CMG503
CMG504
CHOH2015
CHOH2053

site_idDC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE P3S D 500
ChainResidue
CASP54
DGLU133
DGLU135
DGLU219
DGLU227
DGLY272
DHIS276
DARG329
DGLU335
DARG347
DGLU366
DARG368
DADP501
DMG502
DMG503
DMG504
DHOH2059
DHOH2061
DHOH2063
DHOH2078
DHOH2096

site_idDC5
Number of Residues21
DetailsBINDING SITE FOR RESIDUE ADP D 501
ChainResidue
DGLU133
DGLU214
DLYS215
DGLU227
DASN229
DTYR230
DGLN231
DPHE232
DHIS278
DSER280
DARG347
DARG352
DLYS361
DARG364
DGLU366
DP3S500
DMG503
DMG504
DHOH2024
DHOH2058
DHOH2059

site_idDC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE P3S E 500
ChainResidue
DASP54
EGLU133
EGLU135
EGLU219
EGLU227
EGLY272
EGLY274
EHIS276
EARG329
EGLU335
EARG347
EGLU366
EARG368
EADP501
EMG502
EMG503
EMG504
EHOH2051
EHOH2072
EHOH2073
EHOH2074
EHOH2094

site_idDC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE ADP E 501
ChainResidue
EGLY131
EGLU133
EGLU214
ELYS215
EGLU227
EASN229
ETYR230
EGLN231
EPHE232
EHIS278
ESER280
EARG347
EARG352
ELYS361
EARG364
EGLU366
EP3S500
EMG503
EMG504
EHOH2074
EHOH2101
EHOH2121

site_idDC8
Number of Residues21
DetailsBINDING SITE FOR RESIDUE P3S F 500
ChainResidue
EASP54
FGLU133
FGLU135
FGLU219
FGLU227
FGLY272
FHIS276
FARG329
FGLU335
FARG347
FGLU366
FARG368
FADP501
FMG502
FMG503
FMG504
FHOH2027
FHOH2065
FHOH2081
FHOH2105
FHOH2106

site_idDC9
Number of Residues20
DetailsBINDING SITE FOR RESIDUE ADP F 501
ChainResidue
FGLU133
FGLU214
FLYS215
FGLU227
FASN229
FTYR230
FGLN231
FPHE232
FHIS278
FSER280
FARG347
FARG352
FLYS361
FARG364
FGLU366
FP3S500
FMG503
FMG504
FHOH2025
FHOH2105

Functional Information from PROSITE/UniProt
site_idPS00180
Number of Residues19
DetailsGLNA_1 Glutamine synthetase signature 1. FDGSSirgfqsihESDmlL
ChainResidueDetails
APHE53-LEU71

site_idPS00181
Number of Residues16
DetailsGLNA_ATP Glutamine synthetase putative ATP-binding region signature. KPLfgd..NGSGmHchqS
ChainResidueDetails
ALYS265-SER280

site_idPS00182
Number of Residues13
DetailsGLNA_ADENYLATION Glutamine synthetase class-I adenylation site. KIepqapVDKDLY
ChainResidueDetails
ALYS394-TYR406

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues504
DetailsDomain: {"description":"GS beta-grasp","evidences":[{"source":"PROSITE-ProRule","id":"PRU01330","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2220
DetailsDomain: {"description":"GS catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01331","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues36
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16027359","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19695264","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22369127","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2012","firstPage":"620","lastPage":"626","volume":"3","journal":"Med. Chem. Commun.","title":"Synthesis, biological evaluation and X-Ray crystallographic studies of imidazo(1,2-A)pyridine-based Mycobacterium tuberculosis glutamine synthetase inhibitors.","authors":["Nordqvist A.","Nilsson M.T.","Lagerlund O.","Muthas D.","Gising J.","Yahiaoui S.","Odell L.R.","Srinivasa B.R.","Larhed M.","Mowbray S.L.","Karlen A."],"citationCrossReferences":[{"database":"DOI","id":"10.1039/C2MD00310D"}]}},{"source":"PDB","id":"2BVC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WHI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ACF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16027359","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2BVC","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues36
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16027359","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"19695264","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22369127","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2012","firstPage":"620","lastPage":"626","volume":"3","journal":"Med. Chem. Commun.","title":"Synthesis, biological evaluation and X-Ray crystallographic studies of imidazo(1,2-A)pyridine-based Mycobacterium tuberculosis glutamine synthetase inhibitors.","authors":["Nordqvist A.","Nilsson M.T.","Lagerlund O.","Muthas D.","Gising J.","Yahiaoui S.","Odell L.R.","Srinivasa B.R.","Larhed M.","Mowbray S.L.","Karlen A."],"citationCrossReferences":[{"database":"DOI","id":"10.1039/C2MD00310D"}]}},{"source":"PDB","id":"2BVC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WHI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ACF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P12425","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P77961","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P0A1P6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16027359","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22369127","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2012","firstPage":"620","lastPage":"626","volume":"3","journal":"Med. Chem. Commun.","title":"Synthesis, biological evaluation and X-Ray crystallographic studies of imidazo(1,2-A)pyridine-based Mycobacterium tuberculosis glutamine synthetase inhibitors.","authors":["Nordqvist A.","Nilsson M.T.","Lagerlund O.","Muthas D.","Gising J.","Yahiaoui S.","Odell L.R.","Srinivasa B.R.","Larhed M.","Mowbray S.L.","Karlen A."],"citationCrossReferences":[{"database":"DOI","id":"10.1039/C2MD00310D"}]}},{"source":"PDB","id":"2BVC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZXV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ACF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues6
DetailsModified residue: {"description":"O-AMP-tyrosine","evidences":[{"source":"PubMed","id":"15037612","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12146952","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"16027359","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
AASP54
AARG347
AGLU335

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
BASP54
BARG347
BGLU335

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
CASP54
CARG347
CGLU335

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
DASP54
DARG347
DGLU335

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
EASP54
EARG347
EGLU335

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1hto
ChainResidueDetails
FASP54
FARG347
FGLU335

site_idMCSA1
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
AASP54activator, proton acceptor
AGLU133metal ligand
AGLU135metal ligand
AGLU219metal ligand
AGLU227metal ligand
AHIS276metal ligand
AARG347electrostatic stabiliser
AGLU366metal ligand
AARG368electrostatic stabiliser

site_idMCSA2
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
BASP54activator, proton acceptor
BGLU133metal ligand
BGLU135metal ligand
BGLU219metal ligand
BGLU227metal ligand
BHIS276metal ligand
BARG347electrostatic stabiliser
BGLU366metal ligand
BARG368electrostatic stabiliser

site_idMCSA3
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
CASP54activator, proton acceptor
CGLU133metal ligand
CGLU135metal ligand
CGLU219metal ligand
CGLU227metal ligand
CHIS276metal ligand
CARG347electrostatic stabiliser
CGLU366metal ligand
CARG368electrostatic stabiliser

site_idMCSA4
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
DASP54activator, proton acceptor
DGLU133metal ligand
DGLU135metal ligand
DGLU219metal ligand
DGLU227metal ligand
DHIS276metal ligand
DARG347electrostatic stabiliser
DGLU366metal ligand
DARG368electrostatic stabiliser

site_idMCSA5
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
EASP54activator, proton acceptor
EGLU133metal ligand
EGLU135metal ligand
EGLU219metal ligand
EGLU227metal ligand
EHIS276metal ligand
EARG347electrostatic stabiliser
EGLU366metal ligand
EARG368electrostatic stabiliser

site_idMCSA6
Number of Residues9
DetailsM-CSA 537
ChainResidueDetails
FASP54activator, proton acceptor
FGLU133metal ligand
FGLU135metal ligand
FGLU219metal ligand
FGLU227metal ligand
FHIS276metal ligand
FARG347electrostatic stabiliser
FGLU366metal ligand
FARG368electrostatic stabiliser

240971

PDB entries from 2025-08-27

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