Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FSX

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0005737	cellular_component	cytoplasm
A	0005886	cellular_component	plasma membrane
A	0008652	biological_process	amino acid biosynthetic process
A	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0009274	cellular_component	peptidoglycan-based cell wall
A	0016740	molecular_function	transferase activity
A	0016746	molecular_function	acyltransferase activity
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0031402	molecular_function	sodium ion binding
A	0046872	molecular_function	metal ion binding
A	0120226	molecular_function	succinyl-CoA binding
B	0000287	molecular_function	magnesium ion binding
B	0005737	cellular_component	cytoplasm
B	0005886	cellular_component	plasma membrane
B	0008652	biological_process	amino acid biosynthetic process
B	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0009274	cellular_component	peptidoglycan-based cell wall
B	0016740	molecular_function	transferase activity
B	0016746	molecular_function	acyltransferase activity
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0031402	molecular_function	sodium ion binding
B	0046872	molecular_function	metal ion binding
B	0120226	molecular_function	succinyl-CoA binding
C	0000287	molecular_function	magnesium ion binding
C	0005737	cellular_component	cytoplasm
C	0005886	cellular_component	plasma membrane
C	0008652	biological_process	amino acid biosynthetic process
C	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0009274	cellular_component	peptidoglycan-based cell wall
C	0016740	molecular_function	transferase activity
C	0016746	molecular_function	acyltransferase activity
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0031402	molecular_function	sodium ion binding
C	0046872	molecular_function	metal ion binding
C	0120226	molecular_function	succinyl-CoA binding
D	0000287	molecular_function	magnesium ion binding
D	0005737	cellular_component	cytoplasm
D	0005886	cellular_component	plasma membrane
D	0008652	biological_process	amino acid biosynthetic process
D	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0009274	cellular_component	peptidoglycan-based cell wall
D	0016740	molecular_function	transferase activity
D	0016746	molecular_function	acyltransferase activity
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0031402	molecular_function	sodium ion binding
D	0046872	molecular_function	metal ion binding
D	0120226	molecular_function	succinyl-CoA binding
E	0000287	molecular_function	magnesium ion binding
E	0005737	cellular_component	cytoplasm
E	0005886	cellular_component	plasma membrane
E	0008652	biological_process	amino acid biosynthetic process
E	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
E	0009085	biological_process	lysine biosynthetic process
E	0009089	biological_process	lysine biosynthetic process via diaminopimelate
E	0009274	cellular_component	peptidoglycan-based cell wall
E	0016740	molecular_function	transferase activity
E	0016746	molecular_function	acyltransferase activity
E	0019877	biological_process	diaminopimelate biosynthetic process
E	0031402	molecular_function	sodium ion binding
E	0046872	molecular_function	metal ion binding
E	0120226	molecular_function	succinyl-CoA binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACY A 331

Chain	Residue
A	ARG201
A	SER203
A	SER219
C	GLY216

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD A 340

Chain	Residue
A	HOH406
A	HIS94
A	ARG95
A	VAL156
A	PRO157
A	THR158

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY B 331

Chain	Residue
A	ALA242
B	ARG201
B	SER203
B	SER219
B	ILE220
B	GLY222
B	HOH466

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MPD B 340

Chain	Residue
B	HIS94
B	ARG95
B	VAL156
B	PRO157
B	THR158
B	HOH485
B	HOH543

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACY C 331

Chain	Residue
B	ALA242
C	ARG201
C	SER203
C	SER219
C	ILE220
C	GLY222
C	HOH486
C	HOH511

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY D 331

Chain	Residue
D	ARG201
D	SER203
D	GLY216
D	SER219
D	ILE220
D	GLY222
D	ALA242

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD D 340

Chain	Residue
D	HIS94
D	ARG95
D	VAL156
D	PRO157
D	THR158

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG C 332

Chain	Residue
A	ASP166
A	NA334
A	HOH401
B	ASP166
B	HOH401
C	ASP166
C	HOH401

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 332

Chain	Residue
A	GLU183
B	GLU183
C	GLU183

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MG D 332

Chain	Residue
D	ASP166
D	ASP166
D	ASP166
D	NA334
D	NA334
D	NA334
D	HOH401
D	HOH401
D	HOH401

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG D 333

Chain	Residue
D	GLU183
D	GLU183
D	GLU183

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG E 331

Chain	Residue
E	ASP166
E	ASP166
E	ASP166

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG E 332

Chain	Residue
E	GLU183
E	GLU183
E	GLU183

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 333

Chain	Residue
A	HOH512
A	HOH519
D	HOH541

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 333

Chain	Residue
D	HOH511
D	HOH511
D	HOH511
E	SER295
E	SER295
E	SER295

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 332

Chain	Residue
B	HOH534
B	HOH547

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NA A 334

Chain	Residue
A	ASP164
A	ASP166
B	ASP164
B	ASP166
C	ASP164
C	ASP166
C	MG332

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE NA D 334

Chain	Residue
D	ASP164
D	ASP164
D	ASP164
D	ASP166
D	ASP166
D	ASP166
D	MG332
D	MG332
D	MG332

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA E 334

Chain	Residue
E	ASP164
E	ASP164
E	ASP164
E	ASP166
E	ASP166
E	ASP166

site_id	CC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NA B 333

Chain	Residue
B	ASP210

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	5
Details	ACT_SITE: Acyl-anhydride intermediate => ECO:0000305\|PubMed:19394346

Chain	Residue	Details
A	GLU199
B	GLU199
C	GLU199
D	GLU199
E	GLU199

site_id	SWS_FT_FI2
Number of Residues	50
Details	BINDING: BINDING => ECO:0000269\|PubMed:19394346

Chain	Residue	Details
A	ASP166
A	ARG290
B	ASP166
B	GLU183
B	ARG201
B	GLY216
B	SER219
B	ALA242
B	GLU257
B	GLY265
B	LYS277
A	GLU183
B	ARG290
C	ASP166
C	GLU183
C	ARG201
C	GLY216
C	SER219
C	ALA242
C	GLU257
C	GLY265
C	LYS277
A	ARG201
C	ARG290
D	ASP166
D	GLU183
D	ARG201
D	GLY216
D	SER219
D	ALA242
D	GLU257
D	GLY265
D	LYS277
A	GLY216
D	ARG290
E	ASP166
E	GLU183
E	ARG201
E	GLY216
E	SER219
E	ALA242
E	GLU257
E	GLY265
E	LYS277
A	SER219
E	ARG290
A	ALA242
A	GLU257
A	GLY265
A	LYS277

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