5NPP

2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA

> Summary

Summary for 5NPP

DescriptorDNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A, DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3'), MANGANESE (II) ION, ... (10 entities in total)
Functional Keywordstype iia topoisomerase, antibacterial, inhibitor, isomerase
Biological sourceStaphylococcus aureus
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Cellular locationCytoplasm  Q99XG5
Total number of polymer chains6
Total molecular weight170663.15
Authors
Bax, B.D.,Chan, P.F.,Stavenger, R.A. (deposition date: 2017-04-18, release date: 2017-07-12)
Primary citation
Chan, P.F.,Germe, T.,Bax, B.D.,Huang, J.,Thalji, R.K.,Bacque, E.,Checchia, A.,Chen, D.,Cui, H.,Ding, X.,Ingraham, K.,McCloskey, L.,Raha, K.,Srikannathasan, V.,Maxwell, A.,Stavenger, R.A.
Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Proc. Natl. Acad. Sci. U.S.A., 114:E4492-E4500, 2017
PubMed: 28507124 (PDB entries with the same primary citation)
DOI: 10.1073/pnas.1700721114
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.22 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.22790.2%3.5%3.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
B, DDNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit Apolymer69278125.02
UniProt (P66937)
UniProt (Q99XG5)
Pfam (PF00521)
Pfam (PF01751)
Staphylococcus aureus
E, FDNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')polymer82451.62
synthetic construct
A, CDNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')polymer123638.42
synthetic construct
MANGANESE (II) IONnon-polymer54.92
~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamidenon-polymer370.92
GLYCEROLnon-polymer92.19
SODIUM IONnon-polymer23.01
DIMETHYL SULFOXIDEnon-polymer78.11
(1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-onenon-polymer451.51
waterwater18.0843

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight168430.0
Non-Polymers*Number of molecules16
Total molecular weight2233.1
All*Total molecular weight170663.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.22 Å)

Cell axes92.85092.850409.980
Cell angles90.0090.00120.00
SpacegroupP 61
Resolution limits19.89 - 2.22
the highest resolution shell value2.277 - 2.220
R-factor0.1841
R-work0.18180
the highest resolution shell value0.309
R-free0.22690
the highest resolution shell value0.323
RMSD bond length0.015
RMSD bond angle1.781

Data Collection Statistics

Resolution limits19.89 - 2.22
the highest resolution shell value -
Number of reflections97193
Rmerge_l_obs0.111
the highest resolution shell value1.158
Completeness99.1
Redundancy5.2
the highest resolution shell value4.9

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1MICROBATCH293

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
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16binding site for residue MN B 1501
ChainResidue
BASP508
BASP510
BHOH1740
BHOH1765
BHOH1796
DHOH1714

AC29binding site for residue 94K B 1502
ChainResidue
BARG630
BILE633
BGLU634
BVAL1031
BMET1179
BARG1342
BPRO1343
BHOH1826
BHOH1833

AC37binding site for residue GOL B 1503
ChainResidue
BGLU1251
BGLY1255
BARG1256
BHOH1605
BHOH1861
DSER1315
DASN1319

AC47binding site for residue GOL B 1504
ChainResidue
BARG1047
BARG1048
BILE1147
BGLU1156
BHOH1673
BHOH1722
BHOH1746

AC56binding site for residue GOL B 1505
ChainResidue
BGLU1190
BGLU1214
BASP1482
BASP1483
BARG1484
BHOH1721

AC66binding site for residue NA B 1506
ChainResidue
BTYR1322
BLYS1323
BTHR1325
BGLN1328
BHOH1926
DHOH1916

AC75binding site for residue DMS B 1507
ChainResidue
BPHE1097
BMET1113
BGLY1115
BHOH1904
BHOH1963

AC86binding site for residue MN D 1501
ChainResidue
DASP508
DASP510
DHOH1673
DHOH1683
DHOH1738
FHOH112

AC912binding site for residue 94K D 1502
ChainResidue
DARG630
DILE633
DGLU634
DALA637
DVAL1031
DMET1179
DARG1342
DPRO1343
DHOH1672
DHOH1828
DHOH1899
DHOH1965

AD16binding site for residue GOL D 1503
ChainResidue
DPRO1044
DARG1047
DGLU1156
DHOH1688
DHOH1737
DHOH1837

AD28binding site for residue GOL D 1504
ChainResidue
BARG1244
BASN1319
DGLU1251
DGLY1255
DARG1256
DGLN1257
DHOH1678
DHOH1754

AD35binding site for residue GOL D 1505
ChainResidue
DGLY1115
DGLN1267
DHOH1818
DHOH1866
FDC-5

AD43binding site for residue GOL D 1506
ChainResidue
DASP1389
DHIS1390
EDA-8

AD56binding site for residue GOL A 101
ChainResidue
ADG1
ADT2
AHOH216
BSER1084
BHOH1742
EDG-1

AD616binding site for residue 6EJ C 101
ChainResidue
ADT2
ADA3
BALA1068
BGLY1072
BMET1075
BASP1083
BMET1121
BHOH1727
BHOH1855
CDT2
CDA3
CHOH219
DALA1068
DMET1075
DASP1083
DMET1121

AD78binding site for residue GOL C 102
ChainResidue
CDG1
CDT2
CHOH206
CHOH208
DSER1084
DHOH1669
FDA-2
FDG-1

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

site_idNumber of ResiduesDetails
94K_5npp_B_150216~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
ChainResidueligand
BARG63094K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BILE633-GLU63494K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BALA637-TYR63994K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BMET102794K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BILE1030-VAL103194K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BMET117994K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BILE133694K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
BGLY1341-LEU134594K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide

GOL_5npp_B_15048GLYCEROL binding site
ChainResidueligand
BALA1032GOL: GLYCEROL
BPRO1044GOL: GLYCEROL
BARG1047-ARG1048GOL: GLYCEROL
BILE1147GOL: GLYCEROL
BGLU1156-SER1158GOL: GLYCEROL

6EJ_5npp_C_10117(1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
ChainResidueligand
BALA10686EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
BVAL1071-GLY10726EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
BMET10756EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
BASP10836EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
BMET11216EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
DALA10686EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
DVAL1071-GLY10726EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
DMET10756EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
DASP10836EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
DMET11216EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
ADG1-DA36EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
CDT2-DA36EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one

GOL_5npp_A_1018GLYCEROL binding site
ChainResidueligand
BSER1084-SER1085GOL: GLYCEROL
EDA-2-DG-1GOL: GLYCEROL
ADG1-DT2GOL: GLYCEROL
CDC4-DC5GOL: GLYCEROL

DMS_5npp_B_15079DIMETHYL SULFOXIDE binding site
ChainResidueligand
BPHE1097DMS: DIMETHYL SULFOXIDE
BSER1112-GLY1115DMS: DIMETHYL SULFOXIDE
BGLN1267-ASN1269DMS: DIMETHYL SULFOXIDE
EDC-5DMS: DIMETHYL SULFOXIDE

GOL_5npp_B_15057GLYCEROL binding site
ChainResidueligand
BASN1187GOL: GLYCEROL
BTHR1189-GLU1190GOL: GLYCEROL
BGLU1214GOL: GLYCEROL
BASP1482-ARG1484GOL: GLYCEROL

GOL_5npp_B_15036GLYCEROL binding site
ChainResidueligand
BGLU1251-GLY1253GOL: GLYCEROL
BGLY1255-GLN1257GOL: GLYCEROL

94K_5npp_D_150216~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
ChainResidueligand
DARG63094K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DILE633-GLU63494K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DALA637-TYR63994K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DMET102794K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DILE1030-VAL103194K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DMET117994K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DILE133694K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
DGLY1341-LEU134594K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide

GOL_5npp_D_15039GLYCEROL binding site
ChainResidueligand
DVAL1031-ALA1032GOL: GLYCEROL
DPRO1044GOL: GLYCEROL
DARG1047-ARG1048GOL: GLYCEROL
DILE1147GOL: GLYCEROL
DGLU1156-SER1158GOL: GLYCEROL

GOL_5npp_C_1029GLYCEROL binding site
ChainResidueligand
DSER1084-SER1085GOL: GLYCEROL
ADA3-DC5GOL: GLYCEROL
FDA-2-DG-1GOL: GLYCEROL
CDG1-DT2GOL: GLYCEROL

GOL_5npp_D_15059GLYCEROL binding site
ChainResidueligand
DPHE1097GOL: GLYCEROL
DSER1112-GLY1115GOL: GLYCEROL
DGLN1267-ASN1269GOL: GLYCEROL
FDC-5GOL: GLYCEROL

GOL_5npp_D_15044GLYCEROL binding site
ChainResidueligand
DGLU1251GOL: GLYCEROL
DGLY1255-GLN1257GOL: GLYCEROL

GOL_5npp_D_15063GLYCEROL binding site
ChainResidueligand
DILE1386GOL: GLYCEROL
DASP1389-HIS1390GOL: GLYCEROL

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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_FI11O-(5'-phospho-DNA)-tyrosine intermediate. {ECO:0000255|HAMAP-Rule:MF_01897}.
ChainResidueDetails
BTYR324

SWS_FT_FI21O-(5'-phospho-DNA)-tyrosine intermediate. {ECO:0000255|HAMAP-Rule:MF_01897}.
ChainResidueDetails
DTYR324

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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