2R7B

Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004672	molecular_function	protein kinase activity
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0005524	molecular_function	ATP binding
A	0006468	biological_process	protein phosphorylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 360

Chain	Residue
A	GLY91
A	SER92
A	PHE93
A	SER94

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PSE A 361

Chain	Residue
A	LYS257
A	TYR126
A	ARG129
A	ARG204
A	LYS228
A	PHE242

---

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 253 A 701

Chain	Residue
A	ALA109
A	LEU159
A	SER160
A	TYR161
A	ALA162
A	LYS163
A	GLY165
A	LEU212
A	THR222

---

Functional Information from PROSITE/UniProt

site_id	PS00107
Number of Residues	24
Details	PROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. LGEGSFSTVVlArelatsre..........YAIK

Chain	Residue	Details
A	LEU88-LYS111

---

site_id	PS00108
Number of Residues	13
Details	PROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. IiHrDLKpeNILL

Chain	Residue	Details
A	ILE201-LEU213

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	44
Details	Region: {"description":"PIF-pocket","evidences":[{"source":"PubMed","id":"22999883","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12169624","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15741170","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22999883","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22999883","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by autocatalysis","evidences":[{"source":"PubMed","id":"10455013","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11481331","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15772071","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16780920","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2009","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Waridel P.","Quadroni M."]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9Z2A0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by MELK","evidences":[{"source":"PubMed","id":"22544756","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1ir3

Chain	Residue	Details
A	GLU209
A	ASP205

---

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1ir3

Chain	Residue	Details
A	LYS207
A	ASP205

---

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1ir3

Chain	Residue	Details
A	LYS207
A	THR245
A	ASP205

---

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1ir3

Chain	Residue	Details
A	LYS207
A	ASN210
A	ASP205

---