Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LVP

Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket

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
B	0004672	molecular_function	protein kinase activity
B	0004674	molecular_function	protein serine/threonine kinase activity
B	0005524	molecular_function	ATP binding
B	0006468	biological_process	protein phosphorylation
C	0004672	molecular_function	protein kinase activity
C	0004674	molecular_function	protein serine/threonine kinase activity
C	0005524	molecular_function	ATP binding
C	0006468	biological_process	protein phosphorylation
D	0004672	molecular_function	protein kinase activity
D	0004674	molecular_function	protein serine/threonine kinase activity
D	0005524	molecular_function	ATP binding
D	0006468	biological_process	protein phosphorylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	binding site for residue ATP A 500

Chain	Residue
A	GLY89
A	GLU166
A	LEU212
A	HOH609
A	GLY91
A	SER92
A	SER94
A	VAL96
A	ALA109
A	LYS111
A	SER160
A	ALA162

site_id	AC2
Number of Residues	14
Details	binding site for residue ATP B 401

Chain	Residue
B	GLY89
B	GLY91
B	SER92
B	SER94
B	VAL96
B	ALA109
B	LYS111
B	SER160
B	ALA162
B	GLU166
B	LEU212
B	HOH519
B	HOH536
B	HOH549

site_id	AC3
Number of Residues	15
Details	binding site for residue ATP C 401

Chain	Residue
C	GLY89
C	GLY91
C	SER92
C	SER94
C	VAL96
C	ALA109
C	LYS111
C	SER160
C	ALA162
C	GLU166
C	GLU209
C	LEU212
C	HOH504
C	HOH508
C	HOH537

site_id	AC4
Number of Residues	1
Details	binding site for residue CL C 402

Chain	Residue
C	LYS144

site_id	AC5
Number of Residues	12
Details	binding site for residue ATP D 500

Chain	Residue
D	GLY89
D	GLU90
D	GLY91
D	SER92
D	SER94
D	VAL96
D	ALA109
D	LYS111
D	SER160
D	ALA162
D	GLU166
D	LEU212

site_id	AC6
Number of Residues	8
Details	binding site for Di-peptide PHE E 11 and SEP E 12

Chain	Residue
C	ARG131
C	THR148
C	PHE149
C	GLN150
E	PHE8
E	PRO9
E	GLN10
E	TYR13

site_id	AC7
Number of Residues	8
Details	binding site for Di-peptide SEP E 12 and TYR E 13

Chain	Residue
C	LEU145
C	PHE147
C	THR148
C	GLN150
E	PHE8
E	GLN10
E	PHE11
E	SER14

site_id	AC8
Number of Residues	9
Details	binding site for Di-peptide PHE F 11 and SEP F 12

Chain	Residue
A	ARG131
A	THR148
A	PHE149
A	GLN150
A	PHE157
F	PHE8
F	PRO9
F	GLN10
F	TYR13

site_id	AC9
Number of Residues	8
Details	binding site for Di-peptide SEP F 12 and TYR F 13

Chain	Residue
A	SER135
A	PHE147
A	THR148
A	GLN150
F	PRO9
F	GLN10
F	PHE11
F	SER14

site_id	AD1
Number of Residues	9
Details	binding site for Di-peptide PHE G 11 and SEP G 12

Chain	Residue
B	ARG131
B	THR148
B	GLN150
B	PHE157
B	HOH547
G	PHE8
G	PRO9
G	GLN10
G	TYR13

site_id	AD2
Number of Residues	8
Details	binding site for Di-peptide SEP G 12 and TYR G 13

Chain	Residue
B	HOH547
G	PRO9
G	GLN10
G	PHE11
G	SER14
B	PHE147
B	THR148
B	GLN150

site_id	AD3
Number of Residues	10
Details	binding site for Di-peptide PHE H 11 and SEP H 12

Chain	Residue
D	ARG131
D	THR148
D	PHE149
D	GLN150
D	LEU155
D	PHE157
H	PHE8
H	PRO9
H	GLN10
H	TYR13

site_id	AD4
Number of Residues	7
Details	binding site for Di-peptide SEP H 12 and TYR H 13

Chain	Residue
D	SER135
D	LEU145
D	THR148
D	GLN150
H	GLN10
H	PHE11
H	SER14

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	176
Details	Region: {"description":"PIF-pocket","evidences":[{"source":"PubMed","id":"22999883","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
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	28
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	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22999883","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
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	4
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	4
Details	Modified residue: {"description":"Phosphothreonine; by MELK","evidences":[{"source":"PubMed","id":"22544756","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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