2FM5

Crystal structure of PDE4D2 in complex with inhibitor L-869299

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 501

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH602
A	HOH607

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 502

Chain	Residue
A	HOH605
A	HOH606
A	HOH607
A	ASP201
A	HOH603
A	HOH604

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 503

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH603
B	HOH608

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 504

Chain	Residue
B	ASP201
B	HOH604
B	HOH605
B	HOH606
B	HOH607
B	HOH608

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 505

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH604
C	HOH609

---

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 506

Chain	Residue
C	ASP201
C	HOH605
C	HOH606
C	HOH607
C	HOH608
C	HOH609

---

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 507

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH605
D	HOH610

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 508

Chain	Residue
D	ASP201
D	HOH606
D	HOH607
D	HOH608
D	HOH609
D	HOH610

---

site_id	AC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE M99 A 601

Chain	Residue
A	THR271
A	MET273
A	ASP318
A	ASN321
A	PRO322
A	TYR329
A	TRP332
A	THR333
A	ILE336
A	MET357
A	GLN369
A	PHE372
A	ILE376
A	HOH606
A	HOH614
A	HOH615
A	HOH637

---

site_id	BC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE M99 B 602

Chain	Residue
B	THR271
B	MET273
B	ASP318
B	ASN321
B	PRO322
B	TYR329
B	TRP332
B	THR333
B	ILE336
B	MET357
B	GLN369
B	PHE372
B	ILE376
B	HOH615
B	HOH616

---

site_id	BC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE M99 C 603

Chain	Residue
C	THR271
C	MET273
C	ASP318
C	ASN321
C	PRO322
C	TYR329
C	TRP332
C	THR333
C	ILE336
C	MET357
C	GLN369
C	PHE372
C	ILE376
C	HOH605
C	HOH608
C	HOH613
C	HOH615
C	HOH640

---

site_id	BC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE M99 D 604

Chain	Residue
D	MET273
D	ASP318
D	ASN321
D	PRO322
D	TYR329
D	TRP332
D	THR333
D	ILE336
D	MET357
D	GLN369
D	PHE372
D	ILE376
D	HOH639
D	HOH675
D	THR271

---

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

---