SInCRe - Rv3582c

Tuberculist information

Gene name	ispD
Protein function	4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (MEP cytidylyltransferase) (MCT)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	4024.34
Molecular mass(da)	24041.5
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 231

	  		  	1    VVREAGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPA   60
			  	61   DRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVAR  120
			  	121  VVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQR  180
			  	181  GSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG

Known structures in the PDB

	PDB ID	2XWN
	Total residue count	466
	Number of chains	2
	Method	X-RAY
	Resolution	2.9

	PDB ID	3OKR
	Total residue count	931
	Number of chains	5
	Method	X-RAY
	Resolution	2.4

	PDB ID	3Q7U
	Total residue count	462
	Number of chains	2
	Method	X-RAY
	Resolution	2.1

	PDB ID	3Q80
	Total residue count	462
	Number of chains	2
	Method	X-RAY
	Resolution	2

Number of amino acids : 231

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
IspD	PF01128	8-231

Mtb Structural Proteome models

Model Number	1
Model name	Rv3582c_3okr_A
Template	3OKR APDB CREDO
Template coverage	6_231
Template Identity(%)	100.0
Model coverage(%)	97.4
Normalized DOPE score	-1.017

Model Number	2
Model name	Rv3582c_3okr_B
Template	3OKR BPDB CREDO
Template coverage	7_231
Template Identity(%)	100.0
Model coverage(%)	97.0
Normalized DOPE score	-0.902

Model Number	3
Model name	Rv3582c
Template	1VPA APDB CREDO
Template coverage	3_216
Template Identity(%)	34.6
Model coverage(%)	95.7
Normalized DOPE score	-0.222

Structure Models from Chopin

Model Number	1
Profile	c.68.1.13 - 3.90.550.10 Click for model details
zscore	23.16
Residue begin	1
Residue end	231

Binding pockets

STRING

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

Protein interacting with Rv3582c	Gene name	Confidence Score
Rv1011	ispE	0.999
Rv1011	ispE	0.999
Rv3581c	ispF	0.999
Rv2870c	dxr	0.992
Rv2870c	dxr	0.992
Rv2870c	dxr	0.992
Rv2868c	gcpE	0.98
Rv2682c	dxs1	0.966
Rv2682c	dxs1	0.966
Rv2682c	dxs1	0.966
Rv3580c	cysS1	0.965
Rv3580c	cysS1	0.965
Rv1110	lytB2	0.965
Rv3583c	Rv3583c	0.95
Rv3579c	Rv3579c	0.906
Rv3382c	lytB1	0.906
Rv3579c	Rv3579c	0.906

Potential ligand/drug binding sites

No binding sites identified

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
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritolPubChem	0.993	521.307
2-C-methyl-D-erythritol-4-phosphatePubChem	0.944	216.126
Chebi:17764PubChem	0.9	216.126
cytidine triphosphatePubChem	0.889	483.156
ara-CTPPubChem	0.884	483.156
magnesiumPubChem	0.841	24.305
calciumPubChem	0.75	40.078
dimethylallyl diphosphatePubChem	0.73	246.092
cytidine diphosphatePubChem	0.724	403.176
isopentenyl diphosphatePubChem	0.703	246.092