Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6NMZ

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with an intentionally produced fragment degradation product B9D

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	12
Details	binding site for residue KSJ A 301

Chain	Residue
A	THR11
A	SO4303
B	LEU143
B	SO4304
A	LYS15
A	LYS37
A	ASP47
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	KSP302

site_id	AC2
Number of Residues	12
Details	binding site for residue KSP A 302

Chain	Residue
A	THR11
A	LYS15
A	LYS37
A	THR41
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	KSJ301
A	SO4303
B	LEU143
B	SO4304

site_id	AC3
Number of Residues	9
Details	binding site for residue SO4 A 303

Chain	Residue
A	GLY12
A	VAL13
A	GLY14
A	LYS15
A	THR16
A	KSJ301
A	KSP302
A	HOH401
A	HOH412

site_id	AC4
Number of Residues	11
Details	binding site for residue SO4 A 304

Chain	Residue
A	ASP142
A	LEU143
A	GLY144
A	THR145
A	LEU146
A	ASN182
A	HOH402
A	HOH441
B	ALA73
B	KSJ301
B	KSP302

site_id	AC5
Number of Residues	15
Details	binding site for residue KSJ B 301

Chain	Residue
A	LEU143
A	SO4304
B	THR11
B	LYS15
B	THR41
B	ARG45
B	ASP47
B	PRO71
B	ALA73
B	PRO74
B	ALA110
B	GLY111
B	KSP302
B	SO4303
B	HOH446

site_id	AC6
Number of Residues	16
Details	binding site for residue KSP B 302

Chain	Residue
A	LEU143
A	SO4304
B	THR11
B	LYS15
B	THR41
B	ARG45
B	ASP47
B	PRO71
B	MET72
B	ALA73
B	PRO74
B	ALA110
B	GLY111
B	KSJ301
B	SO4303
B	HOH446

site_id	AC7
Number of Residues	7
Details	binding site for residue SO4 B 303

Chain	Residue
B	GLY12
B	VAL13
B	GLY14
B	LYS15
B	THR16
B	KSJ301
B	KSP302

site_id	AC8
Number of Residues	9
Details	binding site for residue SO4 B 304

Chain	Residue
A	VAL115
A	KSJ301
A	KSP302
B	GLY144
B	THR145
B	LEU146
B	ASN147
B	HOH401
B	HOH402

site_id	AC9
Number of Residues	9
Details	binding site for residue SO4 C 301

Chain	Residue
C	HOH424
C	GLY12
C	VAL13
C	GLY14
C	LYS15
C	THR16
C	KSJ303
C	KSP304
C	HOH412

site_id	AD1
Number of Residues	9
Details	binding site for residue SO4 C 302

Chain	Residue
C	GLY144
C	THR145
C	LEU146
C	ASN147
C	HOH401
C	HOH404
D	VAL115
D	KSJ303
D	KSP304

site_id	AD2
Number of Residues	17
Details	binding site for residue KSJ C 303

Chain	Residue
C	THR11
C	GLY12
C	LYS15
C	THR41
C	ARG45
C	ASP47
C	PRO71
C	ALA73
C	PRO74
C	ALA110
C	GLY111
C	VAL115
C	SO4301
C	KSP304
C	HOH424
D	LEU143
D	SO4302

site_id	AD3
Number of Residues	14
Details	binding site for residue KSP C 304

Chain	Residue
C	THR11
C	LYS15
C	THR41
C	PRO71
C	MET72
C	ALA73
C	PRO74
C	ALA110
C	GLY111
C	VAL115
C	SO4301
C	KSJ303
D	LEU143
D	SO4302

site_id	AD4
Number of Residues	9
Details	binding site for residue SO4 D 301

Chain	Residue
D	THR11
D	GLY12
D	VAL13
D	GLY14
D	LYS15
D	THR16
D	KSJ303
D	KSP304
D	HOH402

site_id	AD5
Number of Residues	10
Details	binding site for residue SO4 D 302

Chain	Residue
C	ALA73
C	VAL115
C	KSJ303
C	KSP304
D	LEU143
D	GLY144
D	THR145
D	LEU146
D	ASN147
D	HOH408

site_id	AD6
Number of Residues	16
Details	binding site for residue KSJ D 303

Chain	Residue
C	LEU143
C	SO4302
D	THR11
D	GLY12
D	LYS15
D	THR41
D	MET72
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	SO4301
D	KSP304
D	HOH401
D	HOH404
D	HOH429

site_id	AD7
Number of Residues	15
Details	binding site for residue KSP D 304

Chain	Residue
C	LEU143
C	SO4302
D	THR11
D	GLY12
D	LYS15
D	THR41
D	MET72
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	SO4301
D	KSJ303
D	HOH401
D	HOH404

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)