Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FSY

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA 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	12
Details	BINDING SITE FOR RESIDUE SCA A 331

Chain	Residue
A	GLU257
D	PRO271
D	GLY305
D	HOH580
A	ARG290
A	ARG291
A	ASN292
A	SER293
A	LEU301
B	GLY265
B	ARG267
B	LYS277

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD A 340

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

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SCA B 331

Chain	Residue
B	GLU257
B	ARG290
B	ARG291
B	ASN292
B	SER293
B	GLY305
C	GLY265
C	ARG267

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY B 332

Chain	Residue
B	ARG201
B	SER203
B	SER219
B	ILE220
B	GLY222
B	HOH493
B	HOH503

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD B 340

Chain	Residue
B	HIS94
B	ARG95
B	PRO157
B	THR158
B	HOH542
C	GLU128

site_id	AC6
Number of Residues	26
Details	BINDING SITE FOR RESIDUE SCA A 332

Chain	Residue
A	ARG201
A	SER203
A	SER219
A	MET221
A	THR263
A	GLY265
A	LYS277
A	HOH493
A	HOH503
A	HOH545
A	HOH557
A	HOH570
A	HOH571
A	HOH586
C	GLU199
C	GLY216
C	GLY241
C	ALA242
C	VAL255
C	GLU257
C	ALA258
C	ARG290
C	ARG291
C	ASN292
C	SER293
C	HOH515

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY C 331

Chain	Residue
C	ARG201
C	SER203
C	SER219
C	ILE220
C	GLY222
C	HOH493
C	HOH503

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY D 331

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

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD D 340

Chain	Residue
D	HIS94
D	ARG95
D	VAL156
D	PRO157
D	THR158
D	HOH557

site_id	BC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE SCA E 331

Chain	Residue
E	SER293
E	HOH414
E	HOH418
E	HOH420
E	GLU199
E	ARG201
E	SER203
E	GLY216
E	SER219
E	MET221
E	GLY241
E	ALA242
E	GLU257
E	ALA258
E	THR263
E	GLY265
E	LYS277
E	ARG290
E	ARG291
E	ASN292

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 333

Chain	Residue
A	ASP166
A	NA337
A	HOH401
B	ASP166
B	HOH401
C	ASP166
C	HOH401

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 334

Chain	Residue
A	GLU183
A	HOH547
B	GLU183
B	HOH512
C	GLU183

site_id	BC4
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	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MG D 333

Chain	Residue
D	GLU183
D	GLU183
D	GLU183
D	HOH552
D	HOH552
D	HOH552
D	HOH572
D	HOH572
D	HOH572

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 332

Chain	Residue
E	ASP166
E	ASP166
E	ASP166
E	HOH401
E	HOH401
E	HOH401

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG E 333

Chain	Residue
E	GLU183
E	GLU183
E	GLU183

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 334

Chain	Residue
D	HOH536
D	HOH536
D	HOH536
E	HOH417
E	HOH417
E	HOH417

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 335

Chain	Residue
A	HOH580
A	HOH581
A	HOH582
A	HOH583

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 333

Chain	Residue
B	HOH560
B	HOH561
B	HOH562
B	HOH563
B	HOH564
B	HOH565

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 336

Chain	Residue
A	HOH575
A	HOH576
A	HOH577
A	HOH578
D	HOH579

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NA A 337

Chain	Residue
A	ASP164
A	ASP166
A	MG333
B	ASP164
B	ASP166
C	ASP164
C	ASP166

site_id	CC4
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	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA E 335

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

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 334

Chain	Residue
B	ASP210
B	HOH571
B	HOH571

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	5
Details	Active site: {"description":"Acyl-anhydride intermediate","evidences":[{"source":"PubMed","id":"19394346","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	60
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19394346","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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