6AKR

Crystal structure of the PDE4D catalytic domain in complex with osthole

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	6
Details	binding site for residue ZN A 701

Chain	Residue
A	HIS402
A	HIS438
A	ASP439
A	ASP556
A	ZN702
A	HOH860

---

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN A 702

Chain	Residue
A	HOH826
A	HOH830
A	HOH880
A	ASP439
A	ZN701
A	HOH823

---

site_id	AC3
Number of Residues	9
Details	binding site for residue A0O A 703

Chain	Residue
A	TYR397
A	ASN559
A	TYR567
A	THR571
A	MET575
A	PHE578
A	MET595
A	GLN607
A	PHE610

---

site_id	AC4
Number of Residues	6
Details	binding site for residue ZN B 701

Chain	Residue
B	HIS402
B	HIS438
B	ASP439
B	ASP556
B	ZN702
B	HOH880

---

site_id	AC5
Number of Residues	6
Details	binding site for residue ZN B 702

Chain	Residue
B	ASP439
B	ZN701
B	HOH808
B	HOH827
B	HOH836
B	HOH870

---

site_id	AC6
Number of Residues	8
Details	binding site for residue A0O B 703

Chain	Residue
B	TYR397
B	ASN559
B	THR571
B	ILE574
B	PHE578
B	MET595
B	GLN607
B	PHE610

---

site_id	AC7
Number of Residues	6
Details	binding site for residue ZN C 701

Chain	Residue
C	HIS402
C	HIS438
C	ASP439
C	ASP556
C	ZN702
C	HOH860

---

site_id	AC8
Number of Residues	6
Details	binding site for residue ZN C 702

Chain	Residue
C	ASP439
C	ZN701
C	HOH801
C	HOH814
C	HOH836
C	HOH840

---

site_id	AC9
Number of Residues	7
Details	binding site for residue A0O C 703

Chain	Residue
C	TYR397
C	ASN559
C	THR571
C	ILE574
C	MET595
C	GLN607
C	PHE610

---

site_id	AD1
Number of Residues	6
Details	binding site for residue ZN D 701

Chain	Residue
D	HIS402
D	HIS438
D	ASP439
D	ASP556
D	ZN702
D	HOH878

---

site_id	AD2
Number of Residues	6
Details	binding site for residue ZN D 702

Chain	Residue
D	ASP439
D	ZN701
D	HOH818
D	HOH819
D	HOH831
D	HOH874

---

site_id	AD3
Number of Residues	7
Details	binding site for residue A0O D 703

Chain	Residue
D	ASN559
D	TYR567
D	THR571
D	PHE578
D	MET595
D	GLN607
D	PHE610

---

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	HIS438-PHE449

---

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	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)"}

Chain

Residue

Details

---