4J1R - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GSK3B IN COMPLEX WITH INHIBITOR 15R

Authors :   C. Zhan, Y. Wang, J. Wach, P. Sheehan, C. Zhong, R. Harris, Y. Patskovsky J. Bishop, S. Haggarty, A. Ramek, K. Berry, C. O'Herin, A. N. Koehler, A D. W. Young, S. C. Almo, New York Structural Genomics Research Co (Nysgrc)

Date :   01 Feb 13 (Deposition) - 20 Mar 13 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: C,D  (1x)

Keywords :   Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Kinase, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wang, J. Wach, P. Sheehan, C. Zhong, C. Zhan, R. Harris, S. C. Almo, J. Bishop, S. Haggarty, A. Ramek, K. Berry, C. O'Herin, A. N. Koehler, A. W. Hung, D. W. Young
Fragment-Based Approach Using Diversity-Oriented Synthesis Yields A Gsk3B Inhibitor
To Be Published
PubMed: search

Molecule 1 - GLYCOGEN SYNTHASE KINASE-3 BETA
	Chains	:	A, B, C, D
	EC Number	:	2.7.11.26, 2.7.11.1
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Strain	:	HIGH FIVE CELL
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BD BACULOGOLD PACG2T
	Gene	:	GSK3B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GSK-3 BETA, SERINE/THREONINE-PROTEIN KINASE GSK3B

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	I5R	4	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	4	Ligand/Ion	POTASSIUM ION
3	PO4	4	Ligand/Ion	PHOSPHATE ION
4	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	I5R	1	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	I5R	1	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	I5R	1	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	I5R	1	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 5 (3, 6)

No.	Name	Count	Type	Full Name
1	I5R	2	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 6 (3, 6)

No.	Name	Count	Type	Full Name
1	I5R	2	Ligand/Ion	(2R)-2-(1H-INDOL-3-YLMETHYL)-1,4-DIHYDROPYRIDO[2,3-B]PYRAZIN-3(2H)-ONE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:96 , ARG A:180 , LYS A:205 , PRO A:212 , VAL A:214	BINDING SITE FOR RESIDUE PO4 A 501
02	AC2	SOFTWARE	GLY A:63 , VAL A:70 , VAL A:110 , LEU A:132 , ASP A:133 , TYR A:134 , VAL A:135 , CYS A:199 , HOH A:616 , HOH A:619	BINDING SITE FOR RESIDUE I5R A 502
03	AC3	SOFTWARE	THR A:43 , PRO B:351	BINDING SITE FOR RESIDUE K A 503
04	AC4	SOFTWARE	ARG B:96 , ARG B:180 , LYS B:205 , ASN B:213 , VAL B:214	BINDING SITE FOR RESIDUE PO4 B 501
05	AC5	SOFTWARE	PHE B:67 , VAL B:70 , VAL B:110 , LEU B:132 , ASP B:133 , TYR B:134 , VAL B:135 , CYS B:199 , ASP B:200	BINDING SITE FOR RESIDUE I5R B 502
06	AC6	SOFTWARE	THR B:43	BINDING SITE FOR RESIDUE K B 503
07	AC7	SOFTWARE	ARG C:96 , ARG C:180 , LYS C:205 , ASN C:213 , VAL C:214	BINDING SITE FOR RESIDUE PO4 C 501
08	AC8	SOFTWARE	GLY C:63 , VAL C:70 , VAL C:110 , LEU C:132 , ASP C:133 , TYR C:134 , VAL C:135 , PRO C:136 , LEU C:188 , HOH C:617 , HOH C:620	BINDING SITE FOR RESIDUE I5R C 502
09	AC9	SOFTWARE	THR C:43 , PRO D:351	BINDING SITE FOR RESIDUE K C 503
10	BC1	SOFTWARE	ARG D:96 , ARG D:180 , LYS D:205 , ASN D:213 , VAL D:214	BINDING SITE FOR RESIDUE PO4 D 501
11	BC2	SOFTWARE	GLY D:63 , VAL D:70 , VAL D:110 , LEU D:132 , ASP D:133 , TYR D:134 , VAL D:135 , PRO D:136 , LEU D:188 , CYS D:199 , ASP D:200 , HOH D:622	BINDING SITE FOR RESIDUE I5R D 502
12	BC3	SOFTWARE	THR D:43	BINDING SITE FOR RESIDUE K D 503

(no "SS Bond" information available for 4J1R)

(no "Cis Peptide Bond" information available for 4J1R)

(no "SAP(SNP)/Variant" information available for 4J1R)

(no "PROSITE Motif" information available for 4J1R)

(no "Exon" information available for 4J1R)

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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4j1ra_ A: Glycogen synthase kinase-3 beta (Gsk3b)                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeee.....hhhhhhhh.........eeeeeee...eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhh..............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh........................hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1r A  36 KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSyICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR 383
                                    45        55        65        75        85        95       105       115   ||  129       139       149       159       169       179       189       199       209      |219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379    
                                                                                                             119|                                                                                         216-PTR                                                                                                                                                                   
                                                                                                              124

Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4j1rb_ B: Glycogen synthase kinase-3 beta (Gsk3b)                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee....hhhhhhhhhh.......eeeeeeee.....eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhh............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1r B  36 KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSyICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI 384
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215|      225       235       245       255       265       275       285||     297       307       317       327       337       347       357       367       377       
                                                                                                                                                                                                              216-PTR                                                               286|                                                                                               
                                                                                                                                                                                                                                                                                     289

Chain C from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4j1rc_ C: Glycogen synthase kinase-3 beta (Gsk3b)                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeeeee...eeeeeeee.....eeeeeeee......hhhhhhhh.........eeeeeee....eeeeeee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhh..............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1r C  36 KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSyICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI 384
                                    45        55        65        75        85        95       105       115     ||129       139       149       159       169       179       189       199       209      |219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379     
                                                                                                               121|                                                                                       216-PTR                                                                                                                                                                    
                                                                                                                126

Chain D from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4j1rd_ D: Glycogen synthase kinase-3 beta (Gsk3b)                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeee.....hhhhhhhhhh.......eeeeeee....eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhh..............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1r D  36 KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSyICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI 384
                                    45        55        65        75        85        95       105       115   ||  128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378      
                                                                                                             119|                                                                                          216-PTR                                                                                                                                                                    
                                                                                                              123

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: Glycogen synthase kinase-3 beta (Gsk3b) (35)

Human (Homo sapiens) [TaxId: 9606] (35)

1a	d4j1ra_	A:
1b	d4j1rb_	B:
1c	d4j1rc_	C:
1d	d4j1rd_	D:

(no "CATH Domain" information available for 4J1R)

(no "Pfam Domain" information available for 4J1R)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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(no "Related Entries Specified in the PDB File" available for 4J1R)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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