1PTW

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis

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
C	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
C	0007165	biological_process	signal transduction
C	0008081	molecular_function	phosphoric diester hydrolase activity
D	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
D	0007165	biological_process	signal transduction
D	0008081	molecular_function	phosphoric diester hydrolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 501

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	AMP507

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 502

Chain	Residue
A	HOH513
A	ASP201
A	AMP507
A	HOH508
A	HOH509

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 501

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	AMP508

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 502

Chain	Residue
B	ASP201
B	AMP508
B	HOH509
B	HOH510
B	HOH512

---

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 501

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	AMP509

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 502

Chain	Residue
C	ASP201
C	AMP509
C	HOH513
C	HOH514
C	HOH515

---

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 501

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	AMP510

---

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 502

Chain	Residue
D	ASP201
D	AMP510
D	HOH511
D	HOH512
D	HOH513

---

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE AMP A 507

Chain	Residue
A	TYR159
A	HIS160
A	HIS164
A	ASP201
A	ASP318
A	LEU319
A	ASN321
A	PHE340
A	GLN369
A	PHE372
A	ZN501
A	ZN502
A	HOH510
A	HOH512
A	HOH514

---

site_id	BC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE AMP B 508

Chain	Residue
B	TYR159
B	HIS160
B	HIS200
B	ASP201
B	ASP318
B	LEU319
B	ASN321
B	ILE336
B	GLN369
B	PHE372
B	ZN501
B	ZN502
B	HOH513
B	HOH516

---

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP C 509

Chain	Residue
C	TYR159
C	HIS160
C	ASP201
C	ASP318
C	LEU319
C	ASN321
C	PHE340
C	GLN369
C	PHE372
C	ZN501
C	ZN502
C	HOH510

---

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP D 510

Chain	Residue
D	TYR159
D	HIS160
D	ASP201
D	ASP318
D	LEU319
D	ASN321
D	GLN369
D	PHE372
D	ZN501
D	ZN502
D	HOH514

---

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	4
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	12
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	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":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
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	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)"}

Chain

Residue

Details

---