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5NPK

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

Functional Information from GO Data
ChainGOidnamespacecontents
b0003677molecular_functionDNA binding
b0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
b0005524molecular_functionATP binding
b0006259biological_processDNA metabolic process
b0006265biological_processDNA topological change
B0003677molecular_functionDNA binding
B0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B0005524molecular_functionATP binding
B0006259biological_processDNA metabolic process
B0006265biological_processDNA topological change
d0003677molecular_functionDNA binding
d0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
d0005524molecular_functionATP binding
d0006259biological_processDNA metabolic process
d0006265biological_processDNA topological change
D0003677molecular_functionDNA binding
D0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
D0005524molecular_functionATP binding
D0006259biological_processDNA metabolic process
D0006265biological_processDNA topological change
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue MN B 1501
ChainResidue
BASP508
BASP510
BHOH1724
BHOH1840
BHOH1990
EHOH132

site_idAC2
Number of Residues13
Detailsbinding site for residue 94H B 1502
ChainResidue
BMET1027
BMET1179
BARG1342
BPRO1343
BHOH1683
BHOH1926
BHOH1952
BHOH1970
BHOH2016
DHOH1611
BARG630
BGLU634
BALA637

site_idAC3
Number of Residues4
Detailsbinding site for residue GOL B 1503
ChainResidue
BARG458
BHOH1602
BHOH1870
EDG-1

site_idAC4
Number of Residues5
Detailsbinding site for residue GOL B 1504
ChainResidue
BGLY446
BARG447
BTRP592
BHOH1613
BHOH1978

site_idAC5
Number of Residues6
Detailsbinding site for residue GOL B 1505
ChainResidue
BMET1113
BGLY1115
BGLN1267
BVAL1268
EDC-5
EHOH143

site_idAC6
Number of Residues9
Detailsbinding site for residue 94H B 1506
ChainResidue
BILE1386
BASP1389
BHIS1390
BGLU1393
BARG1414
bARG468
eDA-8
e9JN101
fDT12

site_idAC7
Number of Residues6
Detailsbinding site for residue MN D 1501
ChainResidue
DASP508
DASP510
DHOH1632
DHOH1961
DHOH1968
FHOH106

site_idAC8
Number of Residues6
Detailsbinding site for residue GOL D 1502
ChainResidue
DSER445
DGLY446
DASP589
DTRP592
DHOH1636
DHOH2005

site_idAC9
Number of Residues8
Detailsbinding site for residue 94H D 1503
ChainResidue
DARG630
DGLU634
DALA637
DMET1027
DMET1179
DARG1342
DPRO1343
DHOH1656

site_idAD1
Number of Residues9
Detailsbinding site for residue GOL D 1504
ChainResidue
BLYS1066
BARG1122
BHOH1781
DPRO1080
DHIS1081
DGLY1082
DHOH1658
DHOH1680
DHOH1916

site_idAD2
Number of Residues7
Detailsbinding site for residue GOL D 1505
ChainResidue
DPRO1044
DARG1047
DPRO1157
DHOH1775
DHOH1783
DHOH1867
DHOH1937

site_idAD3
Number of Residues7
Detailsbinding site for residue GOL D 1506
ChainResidue
DTYR1051
DGLU1055
DTYR1078
DGLU1154
DARG1155
DHOH1606
DHOH1794

site_idAD4
Number of Residues4
Detailsbinding site for residue CL D 1507
ChainResidue
DHIS1390
DHOH2114
fDA-8
fHOH110

site_idAD5
Number of Residues6
Detailsbinding site for residue MN b 1501
ChainResidue
bASP508
bASP510
bHOH1641
bHOH1935
bHOH1962
eHOH224

site_idAD6
Number of Residues14
Detailsbinding site for residue 94H b 1502
ChainResidue
bMET1027
bMET1179
bARG1342
bPRO1343
bHOH1802
bHOH1845
bHOH1903
bHOH1986
bHOH2017
dGLU1235
dHOH1609
bARG630
bGLU634
bALA637

site_idAD7
Number of Residues9
Detailsbinding site for residue GOL b 1503
ChainResidue
bMET1075
bPRO1080
bHIS1081
bHOH1653
bHOH1697
bHOH1772
bHOH1841
dARG1122
dPHE1123

site_idAD8
Number of Residues7
Detailsbinding site for residue GOL b 1504
ChainResidue
bPRO1044
bARG1047
bHOH1634
bHOH1656
bHOH1666
bHOH1758
bHOH1820

site_idAD9
Number of Residues8
Detailsbinding site for residue GOL b 1505
ChainResidue
bARG1122
bPHE1123
bHOH1655
bHOH1660
bHOH1706
dMET1075
dPRO1080
dHIS1081

site_idAE1
Number of Residues5
Detailsbinding site for residue SO4 b 1506
ChainResidue
bARG1429
bHOH1627
bHOH1973
dARG1429
dARG1432

site_idAE2
Number of Residues6
Detailsbinding site for residue NA b 1507
ChainResidue
bTYR1322
bLYS1323
bTHR1325
bGLN1328
bHOH1991
bHOH2074

site_idAE3
Number of Residues12
Detailsbinding site for residue 9JN b 1508
ChainResidue
BARG468
BHOH2073
EDA-8
FDT12
bARG1385
bILE1386
bASP1389
bHIS1390
bGLU1393
bARG1414
bLYS1416
b94H1509

site_idAE4
Number of Residues13
Detailsbinding site for residue 94H b 1509
ChainResidue
BARG468
BHOH2073
EDA-8
FDT12
bILE1386
bASP1389
bHIS1390
bGLU1393
bARG1414
bPHE1415
bLYS1416
b9JN1508
bHOH1718

site_idAE5
Number of Residues6
Detailsbinding site for residue MN d 1501
ChainResidue
dASP508
dASP510
dHOH1649
dHOH1843
dHOH1879
fHOH131

site_idAE6
Number of Residues9
Detailsbinding site for residue 94H d 1502
ChainResidue
dARG630
dILE633
dGLU634
dALA637
dMET1027
dMET1179
dARG1342
dPRO1343
dHOH1840

site_idAE7
Number of Residues4
Detailsbinding site for residue GOL d 1503
ChainResidue
dGLY446
dARG447
dASP589
dHOH1607

site_idAE8
Number of Residues7
Detailsbinding site for residue GOL d 1504
ChainResidue
dPRO1044
dARG1047
dARG1048
dGLU1156
dHOH1601
dHOH1653
dHOH1676

site_idAE9
Number of Residues2
Detailsbinding site for residue MN d 1505
ChainResidue
FDA-8
dHIS1390

site_idAF1
Number of Residues11
Detailsbinding site for residue 9JN e 101
ChainResidue
BARG1385
BILE1386
BASP1389
BHIS1390
BGLU1393
BARG1414
B94H1506
BHOH1852
bARG468
eDA-8
fDT12

site_idAF2
Number of Residues9
Detailsbinding site for residue GOL e 102
ChainResidue
bARG458
bGLY459
eDG-1
eDG1
eDT2
eHOH203
eHOH222
fDA3
fDC4

site_idAF3
Number of Residues12
Detailsbinding site for Di-peptide GLN b 1413 and ARG b 1414
ChainResidue
bGLU1393
bTHR1397
bGLU1409
bSER1410
bLEU1411
bGLN1412
bPHE1415
bLYS1416
b9JN1508
b94H1509
bHOH1741
bHOH2094

site_idAF4
Number of Residues12
Detailsbinding site for Di-peptide GLN b 1413 and ARG b 1414
ChainResidue
bGLU1393
bTHR1397
bGLU1409
bSER1410
bLEU1411
bGLN1412
bPHE1415
bLYS1416
b9JN1508
b94H1509
bHOH1741
bHOH2094

Functional Information from PROSITE/UniProt
site_idPS00177
Number of Residues9
DetailsTOPOISOMERASE_II DNA topoisomerase II signature. LVEGDSAGG
ChainResidueDetails
BLEU433-GLY441

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01898
ChainResidueDetails
BGLU435
dGLU435
dASP508
dASP510
BASP508
BASP510
DGLU435
DASP508
DASP510
bGLU435
bASP508
bASP510

site_idSWS_FT_FI2
Number of Residues8
DetailsSITE: Interaction with DNA => ECO:0000255|HAMAP-Rule:MF_01898
ChainResidueDetails
BLYS460
BASN463
DLYS460
DASN463
bLYS460
bASN463
dLYS460
dASN463

site_idSWS_FT_FI3
Number of Residues4
DetailsACT_SITE: O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|HAMAP-Rule:MF_01897
ChainResidueDetails
BPHE1123
DPHE1123
bPHE1123
dPHE1123

225946

PDB entries from 2024-10-09

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