4EOI - JenaLib

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Title :   THR 160 PHOSPHORYLATED CDK2 K89D, Q131E - HUMAN CYCLIN A3 COMPLEX WITH THE INHIBITOR RO3306

Authors :   A. Echalier, E. Cot, A. Camasses, E. Hodimont, F. Hoh, F. Sheinerman, L. Krasinska, D. Fisher

Date :   14 Apr 12 (Deposition) - 06 Feb 13 (Release) - 06 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Protein Kinase, Cell Cycle, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Echalier, E. Cot, A. Camasses, E. Hodimont, F. Hoh, P. Jay, F. Sheinerman, L. Krasinska, D. Fisher
An Integrated Chemical Biology Approach Provides Insight Into Cdk2 Functional Redundancy And Inhibitor Sensitivity.
Chem. Biol. V. 19 1028 2012
PubMed-ID: 22921070 | Reference-DOI: 10.1016/J.CHEMBIOL.2012.06.015

Molecule 1 - CYCLIN-DEPENDENT KINASE 2
	Chains	:	A, C
	EC Number	:	2.7.11.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CDK2, CDKN2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CELL DIVISION PROTEIN KINASE 2, P33 PROTEIN KINASE

Molecule 2 - CYCLIN-A2
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	C-TERMINAL FRAGMENT
	Gene	:	CCNA2, CCN1, CCNA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIN-A

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	1RO	2	Ligand/Ion	(5E)-5-(QUINOLIN-6-YLMETHYLIDENE)-2-[(THIOPHEN-2-YLMETHYL)AMINO]-1,3-THIAZOL-4(5H)-ONE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	SGM	2	Ligand/Ion	MONOTHIOGLYCEROL
4	TPO	2	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	1RO	1	Ligand/Ion	(5E)-5-(QUINOLIN-6-YLMETHYLIDENE)-2-[(THIOPHEN-2-YLMETHYL)AMINO]-1,3-THIAZOL-4(5H)-ONE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	SGM	1	Ligand/Ion	MONOTHIOGLYCEROL
4	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	1RO	1	Ligand/Ion	(5E)-5-(QUINOLIN-6-YLMETHYLIDENE)-2-[(THIOPHEN-2-YLMETHYL)AMINO]-1,3-THIAZOL-4(5H)-ONE
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	SGM	1	Ligand/Ion	MONOTHIOGLYCEROL
4	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:12 , GLY A:13 , ALA A:31 , LYS A:33 , GLU A:81 , PHE A:82 , LEU A:83 , ASP A:86 , GLU A:131 , ASN A:132 , LEU A:134 , ASP A:145 , HOH A:434	BINDING SITE FOR RESIDUE 1RO A 301
2	AC2	SOFTWARE	ARG A:214 , ARG A:217 , LYS A:278	BINDING SITE FOR RESIDUE DMS A 302
3	AC3	SOFTWARE	MET B:189 , CYS B:193 , ARG B:241 , ASP B:305 , HOH B:660	BINDING SITE FOR RESIDUE SGM B 501
4	AC4	SOFTWARE	GLY C:13 , LYS C:33 , GLU C:81 , PHE C:82 , LEU C:83 , ASP C:86 , GLU C:131 , ASN C:132 , LEU C:134 , ASP C:145	BINDING SITE FOR RESIDUE 1RO C 301
5	AC5	SOFTWARE	LYS D:192 , CYS D:193 , ARG D:241 , ASP D:305	BINDING SITE FOR RESIDUE SGM D 501

(no "SS Bond" information available for 4EOI)

Asymmetric Unit

No.	Residues
1	Val A:154	-	Pro A:155
2	Gln B:323	-	Pro B:324
3	Asp B:345	-	Pro B:346
4	Val C:154	-	Pro C:155
5	Gln D:323	-	Pro D:324
6	Asp D:345	-	Pro D:346

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

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

(no "Exon" information available for 4EOI)

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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4eoia_ A: Cyclin-dependent PK, CDK2                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeeeeee....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eoi A   0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKDFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPENLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL 298
                                     9        19        29       |43        53        63        73        83        93       103       113       123       133       143       153      |163       173       183       193       203       213       223       233       243       253       263       273       283       293     
                                                                37|                                                                                                                   160-TPO                                                                                                                                      
                                                                 42

Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4eoib1 B:175-309 Cyclin A                                                                                                             d4eoib2 B:310-432 Cyclin A                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eoi B 175 VPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL 432
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424

Chain C from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4eoic_ C: Cyclin-dependent PK, CDK2                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeee....eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........................hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eoi C   0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKDFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPENLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHL 296
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159|      169       179       189       199       209       219       229       239       249       259       269       279       289       
                                                                                                                                                                                          160-TPO

Chain D from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4eoid1 D:178-309 Cyclin A                                                                                                          d4eoid2 D:310-432 Cyclin A                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eoi D 178 YHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL 432
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cyclin-like (137)

Superfamily: Cyclin-like (137)

Family: Cyclin (117)

Protein domain: Cyclin A (82)

Human (Homo sapiens) [TaxId: 9606] (73)

1a	d4eoib1	B:175-309
1b	d4eoib2	B:310-432
1c	d4eoid1	D:178-309
1d	d4eoid2	D:310-432

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: Cyclin-dependent PK, CDK2 (340)

Human (Homo sapiens) [TaxId: 9606] (336)

2a	d4eoia_	A:
2b	d4eoic_	C:

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

(no "Pfam Domain" information available for 4EOI)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp B:345 - Pro B:346	[ RasMol ]
		Asp D:345 - Pro D:346	[ RasMol ]
		Gln B:323 - Pro B:324	[ RasMol ]
		Gln D:323 - Pro D:324	[ RasMol ]
		Val A:154 - Pro A:155	[ RasMol ]
		Val C:154 - Pro C:155	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2.7.11.22
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 6)

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