Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6NNZ

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 4

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	14
Details	binding site for residue KUD A 301

Chain	Residue
A	THR11
A	KUG302
A	SO4303
A	HOH415
B	LEU143
B	SO4303
A	LYS15
A	THR41
A	ARG45
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	VAL115

site_id	AC2
Number of Residues	15
Details	binding site for residue KUG A 302

Chain	Residue
A	THR11
A	LYS15
A	THR41
A	ARG45
A	MET72
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	VAL115
A	KUD301
A	SO4303
A	HOH415
B	LEU143
B	SO4303

site_id	AC3
Number of Residues	8
Details	binding site for residue SO4 A 303

Chain	Residue
A	GLY12
A	VAL13
A	GLY14
A	LYS15
A	THR16
A	KUD301
A	KUG302
A	HOH425

site_id	AC4
Number of Residues	7
Details	binding site for residue SO4 A 304

Chain	Residue
A	GLY144
A	THR145
A	LEU146
A	ASN147
A	HOH410
B	KUD301
B	KUG302

site_id	AC5
Number of Residues	18
Details	binding site for residue KUD B 301

Chain	Residue
A	LEU143
A	GLY144
A	SO4304
B	THR11
B	GLY12
B	LYS15
B	THR41
B	ARG45
B	PRO71
B	MET72
B	ALA73
B	PRO74
B	ALA110
B	GLY111
B	VAL115
B	KUG302
B	SO4304
B	HOH421

site_id	AC6
Number of Residues	17
Details	binding site for residue KUG B 302

Chain	Residue
A	LEU143
A	SO4304
B	THR11
B	GLY12
B	LYS15
B	THR41
B	ARG45
B	PRO71
B	MET72
B	ALA73
B	PRO74
B	ALA110
B	GLY111
B	VAL115
B	KUD301
B	SO4304
B	HOH421

site_id	AC7
Number of Residues	8
Details	binding site for residue SO4 B 303

Chain	Residue
A	VAL115
A	KUD301
A	KUG302
B	GLY144
B	THR145
B	LEU146
B	ASN147
B	HOH405

site_id	AC8
Number of Residues	7
Details	binding site for residue SO4 B 304

Chain	Residue
B	GLY12
B	VAL13
B	GLY14
B	LYS15
B	THR16
B	KUD301
B	KUG302

site_id	AC9
Number of Residues	18
Details	binding site for residue KUD C 301

Chain	Residue
C	PRO74
C	ALA110
C	GLY111
C	VAL115
C	KUG302
C	SO4303
C	HOH409
C	HOH433
C	HOH434
C	HOH438
D	LEU143
D	GLY144
D	SO4303
C	THR11
C	GLY12
C	LYS15
C	THR41
C	ARG45

site_id	AD1
Number of Residues	17
Details	binding site for residue KUG C 302

Chain	Residue
C	THR11
C	GLY12
C	LYS15
C	THR41
C	ARG45
C	PRO71
C	MET72
C	PRO74
C	ALA110
C	GLY111
C	VAL115
C	KUD301
C	SO4303
C	HOH409
C	HOH433
D	LEU143
D	SO4303

site_id	AD2
Number of Residues	8
Details	binding site for residue SO4 C 303

Chain	Residue
C	GLY12
C	VAL13
C	GLY14
C	LYS15
C	THR16
C	KUD301
C	KUG302
C	HOH409

site_id	AD3
Number of Residues	9
Details	binding site for residue SO4 C 304

Chain	Residue
C	GLY144
C	THR145
C	LEU146
C	ASN147
C	HOH403
C	HOH411
D	VAL115
D	KUD301
D	KUG302

site_id	AD4
Number of Residues	15
Details	binding site for residue KUD D 301

Chain	Residue
C	LEU143
C	GLY144
C	SO4304
D	THR11
D	LYS15
D	THR41
D	MET72
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	VAL115
D	KUG302
D	SO4304
D	HOH402

site_id	AD5
Number of Residues	15
Details	binding site for residue KUG D 302

Chain	Residue
C	LEU143
C	GLY144
C	SO4304
D	THR11
D	LYS15
D	THR41
D	MET72
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	VAL115
D	KUD301
D	SO4304
D	HOH402

site_id	AD6
Number of Residues	9
Details	binding site for residue SO4 D 303

Chain	Residue
C	VAL115
C	KUD301
C	KUG302
D	GLY144
D	THR145
D	LEU146
D	ASN147
D	HOH407
D	HOH412

site_id	AD7
Number of Residues	7
Details	binding site for residue SO4 D 304

Chain	Residue
D	GLY12
D	VAL13
D	GLY14
D	LYS15
D	THR16
D	KUD301
D	KUG302

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)