Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6LRM

Crystal structure of PDE4D catalytic domain in complex with arctigenin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
A	0007165	biological_process	signal transduction
A	0008081	molecular_function	phosphoric diester hydrolase activity
B	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
B	0007165	biological_process	signal transduction
B	0008081	molecular_function	phosphoric diester hydrolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue ZN A 501

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH632
A	HOH742

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 502

Chain	Residue
A	HOH670
A	HOH679
A	HOH769
A	ASP201
A	HOH631
A	HOH632

site_id	AC3
Number of Residues	10
Details	binding site for residue EQC A 503

Chain	Residue
A	HIS160
A	ASN321
A	THR333
A	ILE336
A	MET357
A	GLN369
A	PHE372
A	ILE376
A	HOH644
A	HOH714

site_id	AC4
Number of Residues	2
Details	binding site for residue EDO A 504

Chain	Residue
A	SER355
A	PRO356

site_id	AC5
Number of Residues	3
Details	binding site for residue EDO A 505

Chain	Residue
A	HIS154
A	ASP156
A	PRO205

site_id	AC6
Number of Residues	5
Details	binding site for residue EDO A 506

Chain	Residue
A	ASN115
A	ALA155
A	ASN162
A	ILE163
A	HOH668

site_id	AC7
Number of Residues	3
Details	binding site for residue EDO A 507

Chain	Residue
A	ASN402
A	HOH728
B	ARG330

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO A 508

Chain	Residue
A	LYS262
A	ILE265
A	ASP266
A	HOH645

site_id	AC9
Number of Residues	4
Details	binding site for residue EDO A 509

Chain	Residue
A	THR186
A	GLU189
A	SER259
A	MET263

site_id	AD1
Number of Residues	4
Details	binding site for residue EDO A 510

Chain	Residue
A	THR134
A	LYS136
A	ASN251
A	GLN256

site_id	AD2
Number of Residues	5
Details	binding site for residue EDO A 511

Chain	Residue
A	PHE249
A	ARG257
A	ARG261
A	HOH602
A	HOH713

site_id	AD3
Number of Residues	3
Details	binding site for residue EDO A 512

Chain	Residue
A	GLN327
A	HOH741
B	HOH645

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO A 513

Chain	Residue
A	LEU181
A	ALA183
A	VAL184
A	PHE185
A	ILE190
A	HOH630
A	HOH782

site_id	AD5
Number of Residues	5
Details	binding site for residue EDO A 514

Chain	Residue
A	GLN258
A	HOH602
A	HOH604
B	ILE213
B	ASP225

site_id	AD6
Number of Residues	3
Details	binding site for residue EDO A 515

Chain	Residue
A	LYS290
A	LYS291
A	LEU299

site_id	AD7
Number of Residues	7
Details	binding site for residue EDO A 516

Chain	Residue
A	ARG330
A	GLU366
A	TYR406
A	EDO517
A	HOH724
B	PRO411
B	GLN412

site_id	AD8
Number of Residues	9
Details	binding site for residue EDO A 517

Chain	Residue
A	ARG330
A	THR333
A	ASP334
A	VAL365
A	TYR406
A	EDO516
A	HOH619
A	HOH722
A	HOH724

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO A 518

Chain	Residue
A	ASP374
A	HIS378
A	GLU400
A	HOH650

site_id	AE1
Number of Residues	2
Details	binding site for residue EDO A 519

Chain	Residue
A	PRO179
A	GLY296

site_id	AE2
Number of Residues	6
Details	binding site for residue MG B 501

Chain	Residue
B	ASP201
B	HOH617
B	HOH624
B	HOH657
B	HOH663
B	HOH716

site_id	AE3
Number of Residues	6
Details	binding site for residue ZN B 502

Chain	Residue
B	HIS200
B	ASP201
B	ASP318
B	HOH617
B	HOH681
B	HIS164

site_id	AE4
Number of Residues	11
Details	binding site for residue EQC B 503

Chain	Residue
B	HIS160
B	ASN321
B	THR333
B	ILE336
B	MET357
B	GLN369
B	PHE372
B	ILE376
B	EDO510
B	HOH640
B	HOH680

site_id	AE5
Number of Residues	3
Details	binding site for residue EDO B 504

Chain	Residue
B	SER208
B	PRO356
B	EDO510

site_id	AE6
Number of Residues	6
Details	binding site for residue EDO B 505

Chain	Residue
A	ASP156
B	LEU299
B	LEU300
B	ASP301
B	ASN302
B	ASP305

site_id	AE7
Number of Residues	4
Details	binding site for residue EDO B 506

Chain	Residue
A	ASN224
B	LYS262
B	ASP266
B	HOH636

site_id	AE8
Number of Residues	5
Details	binding site for residue EDO B 507

Chain	Residue
B	LEU175
B	THR178
B	TRP384
B	ASP391
B	ALA392

site_id	AE9
Number of Residues	4
Details	binding site for residue EDO B 508

Chain	Residue
B	PHE249
B	ARG257
B	HOH612
B	HOH623

site_id	AF1
Number of Residues	8
Details	binding site for residue EDO B 509

Chain	Residue
A	GLN407
B	GLU150
B	ASP151
B	TYR153
B	ALA155
B	ASN162
B	HOH613
B	HOH626

site_id	AF2
Number of Residues	9
Details	binding site for residue EDO B 510

Chain	Residue
B	HIS160
B	HIS204
B	GLY206
B	VAL207
B	GLU339
B	PHE340
B	GLN343
B	EQC503
B	EDO504

site_id	AF3
Number of Residues	4
Details	binding site for residue EDO B 511

Chain	Residue
B	ALA235
B	HOH603
B	HOH634
B	HOH709

site_id	AF4
Number of Residues	5
Details	binding site for residue EDO B 512

Chain	Residue
A	LYS367
B	HIS154
B	ASP156
B	VAL157
B	PRO205

site_id	AF5
Number of Residues	1
Details	binding site for residue EDO B 513

Chain	Residue
B	GLU366

Functional Information from PROSITE/UniProt

site_id	PS00126
Number of Residues	12
Details	PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF

Chain	Residue	Details
A	HIS200-PHE211

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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