Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6NN0

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and 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	8
Details	binding site for residue SO4 A 301

Chain	Residue
A	GLY12
A	VAL13
A	GLY14
A	LYS15
A	THR16
A	KSJ302
A	KSP303
A	HOH442

site_id	AC2
Number of Residues	13
Details	binding site for residue KSJ A 302

Chain	Residue
A	LYS15
A	ASP47
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	VAL115
A	SO4301
A	KSP303
A	HOH403
B	LEU143
B	SO4302
A	THR11

site_id	AC3
Number of Residues	16
Details	binding site for residue KSP A 303

Chain	Residue
A	THR11
A	GLY12
A	LYS15
A	THR41
A	ARG45
A	PRO71
A	ALA73
A	PRO74
A	ALA110
A	GLY111
A	VAL115
A	SO4301
A	KSJ302
A	HOH403
B	LEU143
B	SO4302

site_id	AC4
Number of Residues	10
Details	binding site for residue SO4 B 301

Chain	Residue
B	GLY12
B	VAL13
B	GLY14
B	LYS15
B	THR16
B	CTN303
B	KSJ304
B	KSP305
B	HOH420
B	HOH427

site_id	AC5
Number of Residues	9
Details	binding site for residue SO4 B 302

Chain	Residue
A	VAL115
A	KSJ302
A	KSP303
B	GLY144
B	THR145
B	LEU146
B	ASN147
B	HOH405
B	HOH407

site_id	AC6
Number of Residues	10
Details	binding site for residue CTN B 303

Chain	Residue
B	VAL17
B	GLY169
B	LEU196
B	PRO197
B	GLY199
B	ALA200
B	ALA201
B	SO4301
B	HOH406
B	HOH411

site_id	AC7
Number of Residues	14
Details	binding site for residue KSJ B 304

Chain	Residue
A	LEU143
A	GLY144
A	HOH451
B	THR11
B	LYS15
B	ARG45
B	ASP47
B	PRO71
B	ALA73
B	ALA110
B	GLY111
B	SO4301
B	KSP305
B	HOH420

site_id	AC8
Number of Residues	14
Details	binding site for residue KSP B 305

Chain	Residue
A	LEU143
A	GLY144
B	THR11
B	LYS15
B	THR41
B	PRO71
B	MET72
B	ALA73
B	PRO74
B	ALA110
B	GLY111
B	SO4301
B	KSJ304
B	HOH420

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

Chain	Residue
C	KSJ303
C	KSP304
C	HOH413
C	HOH421
C	GLY12
C	VAL13
C	GLY14
C	LYS15
C	THR16

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	HOH403
D	GLY111
D	VAL115
D	KSJ304
D	KSP305

site_id	AD2
Number of Residues	18
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	MET72
C	ALA73
C	PRO74
C	ALA110
C	GLY111
C	SO4301
C	KSP304
C	HOH422
C	HOH427
D	GLY144
D	SO4302

site_id	AD3
Number of Residues	16
Details	binding site for residue KSP C 304

Chain	Residue
C	THR11
C	GLY12
C	LYS15
C	THR41
C	ARG45
C	PRO71
C	MET72
C	ALA73
C	PRO74
C	ALA110
C	GLY111
C	SO4301
C	KSJ303
C	HOH422
D	LEU143
D	SO4302

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

Chain	Residue
D	GLY12
D	VAL13
D	GLY14
D	LYS15
D	THR16
D	CTN303
D	KSJ304
D	KSP305
D	HOH423

site_id	AD5
Number of Residues	8
Details	binding site for residue SO4 D 302

Chain	Residue
C	VAL115
C	KSJ303
C	KSP304
D	GLY144
D	THR145
D	LEU146
D	ASN147
D	HOH402

site_id	AD6
Number of Residues	12
Details	binding site for residue CTN D 303

Chain	Residue
D	GLY12
D	VAL17
D	GLU52
D	GLY169
D	SER170
D	LEU196
D	PRO197
D	ALA198
D	ALA200
D	ALA201
D	SO4301
D	HOH426

site_id	AD7
Number of Residues	12
Details	binding site for residue KSJ D 304

Chain	Residue
C	LEU143
C	SO4302
D	THR11
D	GLY12
D	LYS15
D	ARG45
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	SO4301
D	KSP305

site_id	AD8
Number of Residues	14
Details	binding site for residue KSP D 305

Chain	Residue
C	LEU143
C	SO4302
D	THR11
D	GLY12
D	LYS15
D	THR41
D	ARG45
D	ALA73
D	PRO74
D	ALA110
D	GLY111
D	VAL115
D	SO4301
D	KSJ304

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)