Rv0005

Tuberculist information
Gene namegyrB
Protein functionDNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
Functional category(tuberculist)information pathways
Gene location(kb)5.24
Molecular mass(da)74058.7
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 675
	  		  	1    VAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAG   60
			  	61   YATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGL  120
			  	121  HGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVF  180
			  	181  ETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAES  240
			  	241  TAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSES  300
			  	301  VHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISV  360
			  	361  KVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAA  420
			  	421  RKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILP  480
			  	481  LRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHI  540
			  	541  STLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKK  600
			  	601  INKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARR  660
			  	661  SFITRNAKDVRFLDV

Known structures in the PDB
PDB ID2ZJT
Total residue count494
Number of chains2
MethodX-RAY
Resolution2.8
PDB ID3IG0
Total residue count242
Number of chains1
MethodX-RAY
Resolution2.1
PDB ID3M4I
Total residue count242
Number of chains1
MethodX-RAY
Resolution1.95
PDB ID3ZKB
Total residue count6912
Number of chains16
MethodX-RAY
Resolution2.9
PDB ID3ZKD
Total residue count3456
Number of chains8
MethodX-RAY
Resolution2.95
PDB ID3ZM7
Total residue count2652
Number of chains6
MethodX-RAY
Resolution3.3
1 68 135 202 269 336 403 470 537 604 671 Range: 37 to 178  |  Coverage: 20% HATPase_c Range: 256 to 426  |  Coverage: 25% DNA_gyraseB Range: 454 to 566  |  Coverage: 16% Toprim Range: 600 to 664  |  Coverage: 9% DNA_gyraseB_C Range: 448 to 654  |  Coverage: 30% 1 Range: 48 to 466  |  Coverage: 61% 2 Range: 61 to 262  |  Coverage: 29% 1 Range: 48 to 467  |  Coverage: 62% 2 Range: 295 to 465  |  Coverage: 25% 3 Range: 76 to 217  |  Coverage: 20% 4
Number of amino acids : 675
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
HATPase_cPF0251837-178
DNA_gyraseBPF00204256-426
ToprimPF01751454-566
DNA_gyraseB_CPF00986600-664
Mtb Structural Proteome models
Model Number1
Model nameRv0005_3m4i_A
Template3M4I    APDBCREDO
Template coverage448_654
Template Identity(%)100.0
Model coverage(%)28.9
Normalized DOPE score-1.763

Model Number2
Model nameRv0005
Template1EI1    APDBCREDO
Template coverage2_392
Template Identity(%)48.3
Model coverage(%)58.5
Normalized DOPE score-0.314

Structure Models from Chopin
Model Number1
Profiled.122.1.2 - 3.30.565.10
Click for model details
zscore44.29
Residue begin61
Residue end262
Model Number2
Profiled.122.1.2, d.14.1.3 - 3.30.230.10, 3.30.565.10
Click for model details
zscore30.57
Residue begin48
Residue end467
Model Number3
Profiled.14.1.3
Click for model details
zscore23.67
Residue begin295
Residue end465
Model Number4
Profile3.30.565.10
Click for model details
zscore12.18
Residue begin76
Residue end217
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv0005Gene nameConfidence Score
Rv0006gyrA0.999
Rv0006gyrA0.999
Rv0003recF0.997
Rv0002dnaN0.997
Rv0002dnaN0.997
Rv0002dnaN0.997
Rv0001dnaA0.994
Rv0001dnaA0.994
Rv0667rpoB0.974
Rv0667rpoB0.974
Rv0667rpoB0.974
Rv0667rpoB0.974
Rv0667rpoB0.974
Rv0667rpoB0.974
Rv0440groEL20.973
Rv3924crpmH0.966
Rv0682rpsL0.965
Rv3646ctopA0.964
Rv3646ctopA0.964
Rv3646ctopA0.964
Rv3834cserS0.961
Rv3834cserS0.961
Rv0350dnaK0.956
Rv2150cftsZ0.941
Rv2150cftsZ0.941
Rv2343cdnaG0.929
Rv2343cdnaG0.929
Rv2343cdnaG0.929
Rv2343cdnaG0.929
Rv2343cdnaG0.929
Rv3721cdnaZX0.928
Rv3721cdnaZX0.928
Rv3846sodA0.923
Rv3846sodA0.923
Rv2703sigA0.921
Rv2703sigA0.921
Rv2703sigA0.921
Rv2703sigA0.921
Rv2043cpncA0.92
Rv2580chisS0.91
Rv2580chisS0.91
Rv0668rpoC0.909
Rv0668rpoC0.909
Rv0668rpoC0.909
Rv1649pheS0.909
Rv0668rpoC0.909
Rv1649pheS0.909
Rv0668rpoC0.909
Rv2976cung0.908
Rv2678chemE0.907
Potential ligand/drug binding sites
No binding sites identified
Similarity to known drug target from sensitive sequence analysis
DrugBank IDDrug Name
DB01051DrugBankNovobiocin
List of small molecules tested from TIBLE
  View results in TIBLE page
NameAffinityAssay descriptionDOI
CDD-241NoneNoneNone
CDD-272NoneNoneNone
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Cathepsin K 1TU6PharmMapper3 hydroph + 6 HB + 0 pos/neg + 0 aromLink
Tyrosine-protein phosphatase non-receptor type 1 1JF7PharmMapper2 hydroph + 6 HB + 2 pos/neg + 0 aromLink
Tyrosine-protein phosphatase non-receptor type 1 1NO6PharmMapper2 hydroph + 4 HB + 1 pos/neg + 0 aromLink
Aldose reductase 2DUXPharmMapper4 hydroph + 5 HB + 1 pos/neg + 2 aromLink
Phenylalanine-4-hydroxylase 1DMWPharmMapper1 hydroph + 4 HB + 0 pos/neg + 0 aromLink
Topoisomerase II  PASSPa = 0.855 & SM = CDD-272Link
DNA synthesis  PASSPa = 0.816 & SM = CDD-272Link
DNA gyrase subunit A SEAE_value = 1.6e-52 & MaxTC = 0.68Link
topoisomerase IV [-] SEAE_value = 7.09e-49 & MaxTC = 0.68Link
DNA topoisomerase II alpha SEAE_value = 1.2e-47 & MaxTC = 0.43Link
Topoisomerase IV subunit A SEAE_value = 7.06e-46 & MaxTC = 0.5Link
DNA polymerase III polC-type [-] SEAE_value = 3.11e-35 & MaxTC = 0.68Link
DNA gyrase subunit B SEAE_value = 8.71e-23 & MaxTC = 0.68Link
Taq polymerase 1 SEAE_value = 3.5e-17 & MaxTC = 0.38Link
Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.
Data not available
STITCH interactions  
Chemical NameConfidence scoreMolecular Weight
ofloxacinPubChem0.957361.367
moxifloxacinPubChem0.957401.431
levofloxacinPubChem0.918361.367
novobiocinPubChem0.915611.616
gatifloxacinPubChem0.914375.394
ciprofloxacinPubChem0.913331.342
2-methyl-2,4-pentanediolPubChem0.9118.174
(4s)-2-Methyl-2,4-PentanediolPubChem0.9118.174
sparfloxacinPubChem0.897392.4
nalidixic acidPubChem0.894232.235
clinafloxacinPubChem0.881402.248
coumermycinPubChem0.8541110.08
magnesiumPubChem0.80624.305
rifampicinPubChem0.786822.94
trioctylphosphine oxidePubChem0.782386.635
norfloxacinPubChem0.78319.331
coumarinPubChem0.77146.143
trovafloxacinPubChem0.763416.353
enrofloxacinPubChem0.754359.395
AMPPNPPubChem0.746506.196
sitafloxacinPubChem0.745409.814
sulfatePubChem0.73996.0626
hydron sulfatePubChem0.739196.157
formatePubChem0.73145.0174
SmaIPubChem0.728147.217
resazurinPubChem0.728229.188
Phe-Arg beta-naphthylamide dihydrochloridePubChem0.715446.545
garenoxacinPubChem0.714426.413
gemifloxacinPubChem0.711389.381
flumequinePubChem0.704261.248