Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3R5A

Pseudomonas aeruginosa DapD (PA3666) in complex with D-2-aminopimelate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0005737	cellular_component	cytoplasm
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	0016746	molecular_function	acyltransferase activity
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0046872	molecular_function	metal ion binding
B	0000287	molecular_function	magnesium ion binding
B	0005737	cellular_component	cytoplasm
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	0016746	molecular_function	acyltransferase activity
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0046872	molecular_function	metal ion binding
C	0000287	molecular_function	magnesium ion binding
C	0005737	cellular_component	cytoplasm
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	0016746	molecular_function	acyltransferase activity
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0046872	molecular_function	metal ion binding
D	0000287	molecular_function	magnesium ion binding
D	0005737	cellular_component	cytoplasm
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	0016746	molecular_function	acyltransferase activity
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0046872	molecular_function	metal ion binding
E	0000287	molecular_function	magnesium ion binding
E	0005737	cellular_component	cytoplasm
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	0016746	molecular_function	acyltransferase activity
E	0019877	biological_process	diaminopimelate biosynthetic process
E	0046872	molecular_function	metal ion binding
F	0000287	molecular_function	magnesium ion binding
F	0005737	cellular_component	cytoplasm
F	0008666	molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
F	0009085	biological_process	lysine biosynthetic process
F	0009089	biological_process	lysine biosynthetic process via diaminopimelate
F	0016746	molecular_function	acyltransferase activity
F	0019877	biological_process	diaminopimelate biosynthetic process
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE P0A A 351

Chain	Residue
A	PHE129
C	GLU221
A	ARG191
A	ASN209
A	SER225
A	ALA226
A	HOH381
A	HOH878
C	ARG183
C	MET203

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE P0A A 345

Chain	Residue
A	ARG183
A	MET203
A	MET219
A	GLU221
A	HOH952
B	PHE129
B	ARG191
B	PHE207
B	ASN209
B	SER225
B	ALA226

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE P0A C 351

Chain	Residue
B	ARG183
B	MET203
B	GLU221
C	PHE129
C	ARG191
C	ASN209
C	SER225
C	ALA226
C	HOH800
C	HOH895

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL A 346

Chain	Residue
A	ASN139
A	GLU163
A	HOH359
A	HOH375
A	HOH428
A	HOH818
B	ASN139
B	GLU163
B	HOH998
C	ASN139
C	GLU163

site_id	AC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE P0A D 351

Chain	Residue
D	ARG191
D	ASN209
D	SER225
D	ALA226
D	GLY244
D	THR245
D	LEU246
F	ARG183
F	MET203
F	MET219
F	GLU221

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE P0A E 351

Chain	Residue
D	ARG183
D	GLU221
E	PHE129
E	ARG191
E	ASN209
E	SER225
E	ALA226

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 345

Chain	Residue
D	ASN139
D	HOH382
E	ASN139
E	GLU163
E	HOH376
F	ASN139
F	GLU163

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE P0A F 351

Chain	Residue
E	ARG183
E	MET219
E	GLU221
F	PHE129
F	ARG191
F	PHE207
F	ASN209
F	SER225
F	ALA226

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Acyl-anhydride intermediate => ECO:0000255\|HAMAP-Rule:MF_02122

Chain	Residue	Details
A	GLU221
B	GLU221
C	GLU221
D	GLU221
E	GLU221
F	GLU221

site_id	SWS_FT_FI2
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_02122

Chain	Residue	Details
A	GLU205
B	GLU205
C	GLU205
D	GLU205
E	GLU205
F	GLU205

site_id	SWS_FT_FI3
Number of Residues	48
Details	BINDING: BINDING => ECO:0000305\|PubMed:22359568

Chain	Residue	Details
A	ARG223
B	GLY238
B	SER241
B	ALA264
B	GLU279
B	GLY287
B	LYS304
B	ARG317
C	ARG223
C	GLY238
C	SER241
A	GLY238
C	ALA264
C	GLU279
C	GLY287
C	LYS304
C	ARG317
D	ARG223
D	GLY238
D	SER241
D	ALA264
D	GLU279
A	SER241
D	GLY287
D	LYS304
D	ARG317
E	ARG223
E	GLY238
E	SER241
E	ALA264
E	GLU279
E	GLY287
E	LYS304
A	ALA264
E	ARG317
F	ARG223
F	GLY238
F	SER241
F	ALA264
F	GLU279
F	GLY287
F	LYS304
F	ARG317
A	GLU279
A	GLY287
A	LYS304
A	ARG317
B	ARG223

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