Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FPA

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with dethiobiotin and phosphate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0004141	molecular_function	dethiobiotin synthase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0009102	biological_process	biotin biosynthetic process
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0004141	molecular_function	dethiobiotin synthase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0009102	biological_process	biotin biosynthetic process
B	0016874	molecular_function	ligase activity
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0000287	molecular_function	magnesium ion binding
C	0004141	molecular_function	dethiobiotin synthase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0009102	biological_process	biotin biosynthetic process
C	0016874	molecular_function	ligase activity
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0000287	molecular_function	magnesium ion binding
D	0004141	molecular_function	dethiobiotin synthase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0009102	biological_process	biotin biosynthetic process
D	0016874	molecular_function	ligase activity
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 A5254

Chain	Residue
A	GLY12
A	PO45256
A	VAL13
A	GLY14
A	LYS15
A	THR16
A	GLU108
A	HOH228
A	HOH234
A	MG901

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 A5256

Chain	Residue
A	THR11
A	LYS15
A	LYS37
A	ASP49
A	GLU108
A	ALA110
A	GLY111
A	HOH264
A	MG901
A	PO45254
B	DTB803

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PO4 B5257

Chain	Residue
A	DTB803
B	THR11
B	LYS15
B	LYS37
B	ASP49
B	GLU108
B	GLY109
B	ALA110
B	GLY111
B	HOH269
B	MG901
B	PO45255

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 D5259

Chain	Residue
D	THR11
D	GLY12
D	VAL13
D	GLY14
D	LYS15
D	THR16
D	GLU108
D	HOH231
D	HOH253
D	MG901
D	PO45260

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 D5260

Chain	Residue
C	DTB803
D	THR11
D	LYS15
D	LYS37
D	ASP49
D	GLU108
D	ALA110
D	GLY111
D	MG901
D	PO45259

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 C5261

Chain	Residue
C	THR11
C	LYS15
C	LYS37
C	ASP49
C	GLU108
C	ALA110
C	GLY111
C	MG901
C	PO45262

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 C5262

Chain	Residue
C	GLY12
C	VAL13
C	GLY14
C	LYS15
C	THR16
C	GLU108
C	MG901
C	PO45261

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 B5255

Chain	Residue
B	GLY12
B	VAL13
B	GLY14
B	LYS15
B	THR16
B	GLU108
B	HOH267
B	MG901
B	PO45257

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DTB B 803

Chain	Residue
A	THR11
A	THR41
A	ARG45
A	ASP47
A	ALA73
A	HOH264
A	PO45256
B	LEU143
B	GLY144
B	THR145
B	LEU146
B	ASN147
B	HOH242

site_id	BC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE DTB A 803

Chain	Residue
B	THR11
B	THR41
B	ARG45
B	MET72
B	ALA73
B	ALA110
B	GLY111
B	HOH264
B	PO45257
A	LEU143
A	GLY144
A	THR145
A	LEU146
A	ASN147
A	ASN182

site_id	BC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE DTB C 803

Chain	Residue
C	LEU143
C	GLY144
C	THR145
C	LEU146
C	ASN147
C	HOH276
C	HOH277
D	THR11
D	THR41
D	ARG45
D	ASP47
D	ALA73
D	VAL115
D	PO45260

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 901

Chain	Residue
D	THR16
D	ASP49
D	GLU108
D	PO45259
D	PO45260

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 901

Chain	Residue
B	THR16
B	ASP49
B	GLU108
B	PO45255
B	PO45257

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 901

Chain	Residue
A	THR16
A	ASP49
A	GLU108
A	PO45254
A	PO45256

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG C 901

Chain	Residue
C	THR16
C	LYS37
C	ASP49
C	GLU108
C	HOH241
C	PO45261
C	PO45262

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	40
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25801336","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30289406","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2018","firstPage":"10774","lastPage":"10783","volume":"8","journal":"ACS Catal.","title":"Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes.","authors":["Thompson A.P.","Salaemae W.","Pederick J.L.","Abell A.D.","Booker G.W.","Bruning J.B.","Polyak S.W."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/acscatal.8b03475"}]}},{"source":"PDB","id":"4WOP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E05","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E06","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30289406","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2018","firstPage":"10774","lastPage":"10783","volume":"8","journal":"ACS Catal.","title":"Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes.","authors":["Thompson A.P.","Salaemae W.","Pederick J.L.","Abell A.D.","Booker G.W.","Bruning J.B.","Polyak S.W."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/acscatal.8b03475"}]}},{"source":"PDB","id":"3FPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CZB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CZC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CZD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CZE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E05","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E06","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2018","firstPage":"10774","lastPage":"10783","volume":"8","journal":"ACS Catal.","title":"Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes.","authors":["Thompson A.P.","Salaemae W.","Pederick J.L.","Abell A.D.","Booker G.W.","Bruning J.B.","Polyak S.W."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/acscatal.8b03475"}]}},{"source":"PDB","id":"3FMF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FMI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2018","firstPage":"10774","lastPage":"10783","volume":"8","journal":"ACS Catal.","title":"Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes.","authors":["Thompson A.P.","Salaemae W.","Pederick J.L.","Abell A.D.","Booker G.W.","Bruning J.B.","Polyak S.W."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/acscatal.8b03475"}]}},{"source":"PDB","id":"3FMF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FMI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30289406","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2018","firstPage":"10774","lastPage":"10783","volume":"8","journal":"ACS Catal.","title":"Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes.","authors":["Thompson A.P.","Salaemae W.","Pederick J.L.","Abell A.D.","Booker G.W.","Bruning J.B.","Polyak S.W."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/acscatal.8b03475"}]}},{"source":"PDB","id":"6CVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6CVU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E05","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6E06","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)