4IB5 - JenaLib

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Title :   STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT IN COMPLEX WITH A CK2BETA-COMPETITIVE CYCLIC PEPTIDE

Authors :   J. Raaf, B. Guerra, I. Neundorf, B. Bopp, O. -G. Issinger, J. Jose, M. Pie K. Niefind

Date :   08 Dec 12 (Deposition) - 20 Mar 13 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: C,F  (1x)
Biol. Unit 4: G  (1x)

Keywords :   Protein Kinase Fold, Protein Phosphorylation, Binding Of Ck2Beta, Phosphorylation, Nucleus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Raaf, B. Guerra, I. Neundorf, B. Bopp, O. G. Issinger, J. Jose, M. Pietsch, K. Niefind
First Structure Of Protein Kinase Ck2 Catalytic Subunit Wit An Effective Ck2 Beta-Competitive Ligand
Acs Chem. Biol. V. 8 901 2013
PubMed-ID: 23474121 | Reference-DOI: 10.1021/CB3007133
(for further references see the PDB file header)

Molecule 1 - CASEIN KINASE II SUBUNIT ALPHA
	Chains	:	A, B, C
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-355
	Gene	:	CSNK2A1, CK2A1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CK II ALPHA

Molecule 2 - CK2BETA-DERIVED CYCLIC PEPTIDE
	Chains	:	D, E, F, G
	Engineered	:	YES
	Other Details	:	THE MOLECULE WAS SYNTHESIZED BY SOLID-PHASE PEPTIDE SYNTHESIS.
	Synthetic	:	YES

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	G
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C			F
Biological Unit 4 (1x)	:							G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	GOL	9	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	5	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:68 , PHE A:113 , ILE A:174 , ASP A:175 , HOH A:503	BINDING SITE FOR RESIDUE GOL A 401
02	AC2	SOFTWARE	ASN A:16 , THR A:17 , ARG A:43 , LYS A:44 , LEU A:45 , GLY A:46 , HIS A:183 , HOH A:573 , HOH A:654	BINDING SITE FOR RESIDUE GOL A 402
03	AC3	SOFTWARE	TYR A:39 , ALA A:98 , HOH A:590 , HOH A:593 , HOH A:607 , HOH B:510	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	ILE A:94 , ILE A:95 , THR A:96 , GLU A:114 , HIS A:115 , ARG A:172	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	ASP A:156 , LYS A:158 , SER A:194	BINDING SITE FOR RESIDUE GOL A 405
06	AC6	SOFTWARE	HIS A:148 , ALA A:315 , HOH A:517 , HOH A:541	BINDING SITE FOR RESIDUE CL A 406
07	AC7	SOFTWARE	ARG A:80 , ARG A:155 , HOH A:528	BINDING SITE FOR RESIDUE CL A 407
08	AC8	SOFTWARE	ARG B:47 , VAL B:53 , VAL B:66 , LYS B:68 , ILE B:95 , PHE B:113 , ILE B:174 , ASP B:175 , HOH B:514 , HOH B:600	BINDING SITE FOR RESIDUE GOL B 401
09	AC9	SOFTWARE	LYS C:49 , ASP C:156 , LYS C:158 , SER C:194	BINDING SITE FOR RESIDUE GOL C 401
10	BC1	SOFTWARE	LYS C:68 , ILE C:174 , ASP C:175	BINDING SITE FOR RESIDUE GOL C 402
11	BC2	SOFTWARE	SER B:194 , HOH B:570 , GLU C:252 , ASP C:256	BINDING SITE FOR RESIDUE GOL C 403
12	BC3	SOFTWARE	HIS C:148 , THR C:314 , ALA C:315 , HOH C:520 , HOH C:544	BINDING SITE FOR RESIDUE CL C 404
13	BC4	SOFTWARE	PRO A:6 , GLN A:36 , TYR A:39 , GLN A:40 , LEU A:41 , GLU A:52 , PHE A:54 , VAL A:67 , ILE A:69 , LYS A:71 , VAL A:101 , ASP A:103 , HOH A:554 , HOH A:591 , TYR C:146 , ASP C:271 , HOH D:203 , HOH D:204 , HOH D:205 , HOH D:206	BINDING SITE FOR CHAIN D OF CK2BETA-DERIVED CYCLIC PEPTIDE
14	BC5	SOFTWARE	GLN B:36 , TYR B:39 , GLN B:40 , LEU B:41 , GLU B:52 , ILE B:57 , ILE B:69 , VAL B:101 , ASP B:103 , HOH B:509 , PRO C:322 , TYR C:325 , LYS C:329 , HOH E:203 , HOH E:204 , LEU G:187	BINDING SITE FOR CHAIN E OF CK2BETA-DERIVED CYCLIC PEPTIDE
15	BC6	SOFTWARE	GLN C:36 , TYR C:39 , GLN C:40 , LEU C:41 , GLU C:52 , VAL C:101 , ASP C:103 , THR C:108	BINDING SITE FOR CHAIN F OF CK2BETA-DERIVED CYCLIC PEPTIDE
16	BC7	SOFTWARE	VAL B:42 , ARG B:43 , LYS B:44 , PHE B:54 , ARG C:280 , GLU C:282 , PRO C:295 , ASP C:299 , PRO C:322 , ILE E:192 , HOH G:201	BINDING SITE FOR CHAIN G OF CK2BETA-DERIVED CYCLIC PEPTIDE

Asymmetric Unit

No.	Residues
1	D:185	-	D:195
2	E:185	-	E:195
3	F:185	-	F:195
4	G:185	-	G:195

Asymmetric Unit

No.	Residues
1	Lys A:71	-	Pro A:72
2	Glu A:230	-	Pro A:231
3	Lys B:71	-	Pro B:72
4	Glu B:230	-	Pro B:231
5	Glu C:230	-	Pro C:231

(no "SAP(SNP)/Variant" information available for 4IB5)

(no "PROSITE Motif" information available for 4IB5)

(no "Exon" information available for 4IB5)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhh.....hhh.eeeeeeee.....eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh.......eeeeee......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ib5 A   2 SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQA 332
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhh.....hhh.eeeeee........eeeeee.....eeeeee....hhhhhhhhhhhhhhhh.......eeeeee......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.........hhhhhh...hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ib5 B   3 GPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQ 331
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

Chain C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhh.....hhh.eeeeeeee....eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.......eeeeee......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.........hhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ib5 C   2 SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQAR 333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain D from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ..ee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4ib5 D 184 GCRLYGFKIHGCG 196
                                   193

Chain E from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ..ee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4ib5 E 184 GCRLYGFKIHGCG 196
                                   193

Chain F from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ..ee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4ib5 F 184 GCRLYGFKIHGCG 196
                                   193

Chain G from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4ib5 G 184 GCRLYGFKIHGCG 196
                                   193

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4IB5)

(no "CATH Domain" information available for 4IB5)

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Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:230 - Pro A:231	[ RasMol ]
		Glu B:230 - Pro B:231	[ RasMol ]
		Glu C:230 - Pro C:231	[ RasMol ]
		Lys A:71 - Pro A:72	[ RasMol ]
		Lys B:71 - Pro B:72	[ RasMol ]

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1jwh	CK2 HOLOENZYME
1pjk	ROOM TEMPERATURE STRUCTURE OF HUMAN CK2 CATALYTIC SUBUNIT
2pvr	LOW TEMPERATURE STRUCTURE OF HUMAN CK2 CATALYTIC SUBUNIT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (16, 16)

SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

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