SInCRe - Rv0938

Tuberculist information

Gene name	ligD
Protein function	ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase)
Functional category(tuberculist)	information pathways
Gene location(kb)	1046.14
Molecular mass(da)	83572.4
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 759

	  		  	1    MGSASEQRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQ   60
			  	61   PAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAE  120
			  	121  PGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLY  180
			  	181  TPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAP  240
			  	241  YSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDADAPVADRLTRY  300
			  	301  RRMRDASKTPEPIPTAKPVTGDGNTFVIQEHHARRPHYDFRLECDGVLVSWAVPKNLPDN  360
			  	361  TSVNHLAIHTEDHPLEYATFEGAIPSGEYGAGKVIIWDSGTYDTEKFHDDPHTGEVIVNL  420
			  	421  HGGRISGRYALIRTNGDRWLAHRLKNQKDQKVFEFDNLAPMLATHGTVAGLKASQWAFEG  480
			  	481  KWDGYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVP  540
			  	541  SFSQMQNRGRDTRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELLPGDG  600
			  	601  AQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDKHWNTQEVVIGGWRAGEGGRSSGV  660
			  	661  GSLLMGIPGPGGLQFAGRVGTGLSERELANLKEMLAPLHTDESPFDVPLPARDAKGITYV  720
			  	721  KPALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVRE

Known structures in the PDB

	PDB ID	1VS0
	Total residue count	620
	Number of chains	2
	Method	X-RAY
	Resolution	2.4

	PDB ID	2IRU
	Total residue count	606
	Number of chains	2
	Method	X-RAY
	Resolution	1.65

	PDB ID	2IRX
	Total residue count	303
	Number of chains	1
	Method	X-RAY
	Resolution	1.8

	PDB ID	2IRY
	Total residue count	606
	Number of chains	2
	Method	X-RAY
	Resolution	1.78

	PDB ID	2R9L
	Total residue count	640
	Number of chains	6
	Method	X-RAY
	Resolution	2.4

	PDB ID	3PKY
	Total residue count	624
	Number of chains	4
	Method	X-RAY
	Resolution	3.1

	PDB ID	4MKY
	Total residue count	1272
	Number of chains	12
	Method	X-RAY
	Resolution	2.4

Number of amino acids : 759

Domains assigned based on sequence.

Mtb Structural proteome models

CHOPIN models

Profile-based domain assignment

Structural/Functional domain family	Pfam acc.no./SCOP ID	Domain Region
DNA_primase_S	PF01896	136-257
LigD_N	PF13298	329-433
DNA_ligase_A_M	PF01068	460-637
DNA_ligase_A_C	PF04679	656-751

Mtb Structural Proteome models

Model Number	1
Model name	Rv0938_2iru_A
Template	2IRU APDB CREDO
Template coverage	6_291
Template Identity(%)	100.0
Model coverage(%)	37.5
Normalized DOPE score	-1.647

Model Number	2
Model name	Rv0938_2r9l_A
Template	2R9L APDB CREDO
Template coverage	6_292
Template Identity(%)	100.0
Model coverage(%)	37.6
Normalized DOPE score	-1.6

Model Number	3
Model name	Rv0938_1vs0_A
Template	1VS0 APDB CREDO
Template coverage	453_759
Template Identity(%)	100.0
Model coverage(%)	40.3
Normalized DOPE score	-1.41

Model Number	4
Model name	Rv0938
Template	1VS0 APDB CREDO
Template coverage	453_759
Template Identity(%)	100.0
Model coverage(%)	40.3
Normalized DOPE score	-1.205

Model Number	5
Model name	Rv0938.1
Template	2FAO APDB CREDO
Template coverage	549_835
Template Identity(%)	26.5
Model coverage(%)	38.7
Normalized DOPE score	-0.076

Model Number	6
Model name	Rv0938.2
Template	1X9N APDB CREDO
Template coverage	282_888
Template Identity(%)	17.5
Model coverage(%)	81.3
Normalized DOPE score	0.935

Structure Models from Chopin

Model Number	1
Profile	d.142.2.1 Click for model details
zscore	23.98
Residue begin	452
Residue end	644

Model Number	2
Profile	b.40.4.6, d.142.2.1 - 2.40.50.140, 3.30.1490.70, 3.30.470.30 Click for model details
zscore	21.85
Residue begin	449
Residue end	748

Model Number	3
Profile	a.235.1.1, b.40.4.6, d.142.2.1 - 1.10.3260.10, 2.40.50.140, 3.30.1490.70, 3.30.470.30 Click for model details
zscore	20.54
Residue begin	5
Residue end	759

Model Number	4
Profile	3.30.470.30 Click for model details
zscore	8.8
Residue begin	208
Residue end	389

Model Number	5
Profile	d.264.1.2 Click for model details
zscore	8.7
Residue begin	72
Residue end	279

Model Number	6
Profile	b.40.4.6 Click for model details
zscore	5.76
Residue begin	656
Residue end	751

Binding pockets

STRING

Cytoscape Web will replace the contents of this div with protein-protein interaction network.

Protein interacting with Rv0938	Gene name	Confidence Score
Rv0937c	mku	0.991
Rv3014c	ligA	0.902
Rv3014c	ligA	0.902
Rv3014c	ligA	0.902
Rv3014c	ligA	0.902
Rv3014c	ligA	0.902

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv0938_1vs0_A	1	2pgr_DCF_A_501 PDB CREDO	0.570	0.217	0.570	0.004
Rv0938_1vs0_A	1	2zi9_CL9_A_401 PDB CREDO	0.544	0.252	0.544	0.006
Rv0938_1vs0_A	1	1klm_SPP_A_999 PDB CREDO	0.553	0.239	0.533	0.007
Rv0938_1vs0_A	1	2a7q_CFB_A_328 PDB CREDO	0.566	0.222	0.525	0.007
Rv0938_1vs0_A	1	1a4l_DCF_A_353 PDB CREDO	0.536	0.264	0.517	0.008
Rv0938_1vs0_A	1	1a4l_DCF_C_1353 PDB CREDO	0.535	0.265	0.516	0.009
Rv0938_1vs0_A	1	1a4l_DCF_D_1853 PDB CREDO	0.534	0.267	0.515	0.009
Rv0938.2	17	3ua1_08Y_A_600 PDB CREDO	0.578	0.206	0.511	0.009
Rv0938_1vs0_A	1	1a4l_DCF_B_853 PDB CREDO	0.527	0.277	0.508	0.010
Rv0938_2r9l_A	8	1xkk_FMM_A_91 PDB CREDO	0.662	0.113	0.508	0.010
Rv0938_1vs0_A	1	2ya7_ZMR_D_1776 PDB CREDO	0.521	0.286	0.503	0.010

Similarity to known drug target from sensitive sequence analysis

No drug targets

List of small molecules tested from TIBLE

Data not available

Off-target activity - ligand based from TIBLE

Data not available

Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.

Data not available

STITCH interactions

Chemical Name	Confidence score	Molecular Weight
manganesePubChem	0.961	54.938
chloridePubChem	0.943	35.453
diethylene glycolPubChem	0.943	106.12
zincPubChem	0.9	65.409
guanosine triphosphatePubChem	0.9	523.18
SeMetPubChem	0.9	196.106
polyethylene glycolPubChem	0.9	62.0678
deoxyguanosine triphosphatePubChem	0.9	507.181
magnesiumPubChem	0.9	24.305
selenomethioninePubChem	0.9	196.106
ethylene glycol; hydronPubChem	0.9	63.0758