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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR CX-5279

Authors :   R. Battistutta, E. Papinutto, G. Lolli, F. Pierre, M. Haddach, D. M. Ryc

Date :   09 Mar 11 (Deposition) - 07 Dec 11 (Release) - 29 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   Kinase, Ck2-Inhibitor Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Battistutta, G. Cozza, F. Pierre, E. Papinutto, G. Lolli, S. Sarno, S. E. O'Brien, A. Siddiqui-Jain, M. Haddach, K. Anderes, D. M. Ryckman F. Meggio, L. A. Pinna
Unprecedented Selectivity And Structural Determinants Of A New Class Of Protein Kinase Ck2 Inhibitors In Clinical Trials For The Treatment Of Cancer.
Biochemistry V. 50 8478 2011
PubMed-ID: 21870818 | Reference-DOI: 10.1021/BI2008382
(for further references see the PDB file header)

Molecule 1 - CASEIN KINASE II SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-337
	Gene	:	CSNK2A1, CK2A1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CK II ALPHA

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 15)

No.	Name	Count	Type	Full Name
1	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
2	FU9	1	Ligand/Ion	3-(CYCLOPROPYLAMINO)-5-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}PYRIMIDO[4,5-C]QUINOLINE-8-CARBOXYLICACID
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:45 , GLY A:46 , ARG A:47 , VAL A:53 , VAL A:66 , LYS A:68 , PHE A:113 , GLU A:114 , HIS A:115 , VAL A:116 , ASN A:118 , MET A:163 , ILE A:174 , ASP A:175 , EDO A:345 , EDO A:351 , HOH A:370 , HOH A:381 , HOH A:616 , HOH A:636	BINDING SITE FOR RESIDUE FU9 A 338
02	AC2	SOFTWARE	ARG A:80 , ARG A:155 , ASN A:189 , VAL A:192 , HOH A:369 , HOH A:677	BINDING SITE FOR RESIDUE SO4 A 339
03	AC3	SOFTWARE	ARG A:191 , LYS A:198 , ASN A:238 , PEG A:343	BINDING SITE FOR RESIDUE SO4 A 340
04	AC4	SOFTWARE	ASP A:253 , ARG A:278 , ARG A:306 , TYR A:307 , ASP A:308 , HOH A:397 , HOH A:442 , HOH A:465	BINDING SITE FOR RESIDUE SO4 A 341
05	AC5	SOFTWARE	LYS A:170 , ARG A:172 , HOH A:428 , HOH A:463 , HOH A:649	BINDING SITE FOR RESIDUE SO4 A 342
06	AC6	SOFTWARE	SER A:194 , ARG A:195 , TYR A:196 , SO4 A:340 , HOH A:433 , HOH A:619	BINDING SITE FOR RESIDUE PEG A 343
07	AC7	SOFTWARE	GLN A:36 , TYR A:39 , VAL A:101 , ASP A:103 , PRO A:104 , ARG A:280	BINDING SITE FOR RESIDUE EDO A 344
08	AC8	SOFTWARE	ASN A:118 , ASP A:120 , HIS A:160 , FU9 A:338 , EDO A:348 , EDO A:351	BINDING SITE FOR RESIDUE EDO A 345
09	AC9	SOFTWARE	ASP A:37 , PRO A:295 , HIS A:321 , HOH A:620	BINDING SITE FOR RESIDUE EDO A 346
10	BC1	SOFTWARE	PHE A:232 , HOH A:372 , HOH A:573 , HOH A:621 , HOH A:668	BINDING SITE FOR RESIDUE EDO A 347
11	BC2	SOFTWARE	ASN A:118 , THR A:119 , ASP A:120 , PHE A:121 , PRO A:159 , VAL A:162 , MET A:163 , ILE A:164 , EDO A:345	BINDING SITE FOR RESIDUE EDO A 348
12	BC3	SOFTWARE	LYS A:158 , HIS A:160 , SER A:194 , EDO A:350 , HOH A:618 , HOH A:619	BINDING SITE FOR RESIDUE EDO A 349
13	BC4	SOFTWARE	PRO A:159 , PHE A:197 , GLU A:230 , EDO A:349 , HOH A:618	BINDING SITE FOR RESIDUE EDO A 350
14	BC5	SOFTWARE	ASN A:118 , FU9 A:338 , EDO A:345 , HOH A:455 , HOH A:575	BINDING SITE FOR RESIDUE EDO A 351
15	BC6	SOFTWARE	PRO A:104 , ARG A:278 , LYS A:279 , ASP A:302 , HOH A:531 , HOH A:642 , HOH A:679	BINDING SITE FOR RESIDUE EDO A 352

(no "SS Bond" information available for 3R0T)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:230	-	Pro A:231

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_077045	R	47	Q	CSK21_HUMAN	Disease (OCNDS)	869312845	A	R	47	Q
2	UniProt	VAR_077046	Y	50	S	CSK21_HUMAN	Disease (OCNDS)	869312849	A	Y	50	S
3	UniProt	VAR_077047	D	175	G	CSK21_HUMAN	Disease (OCNDS)	869312848	A	D	175	G
4	UniProt	VAR_077048	K	198	R	CSK21_HUMAN	Disease (OCNDS)	869312840	A	K	198	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	CSK21_HUMAN	45-68	1	A:45-68
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CSK21_HUMAN	152-164	1	A:152-164

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000349736	1b	ENSE00001937660	chr20:524465-524316	150	CSK21_HUMAN	-	0	0	-	-
1.3	ENST00000349736	3	ENSE00001709328	chr20:489304-489095	210	CSK21_HUMAN	1-34	34	1	A:3-34	32
1.4	ENST00000349736	4	ENSE00001688643	chr20:485873-485762	112	CSK21_HUMAN	34-71	38	1	A:34-71	38
1.5	ENST00000349736	5	ENSE00001705871	chr20:480578-480477	102	CSK21_HUMAN	72-105	34	1	A:72-105	34
1.6	ENST00000349736	6	ENSE00001598088	chr20:479949-479899	51	CSK21_HUMAN	106-122	17	1	A:106-122	17
1.7	ENST00000349736	7	ENSE00001618963	chr20:478424-478365	60	CSK21_HUMAN	123-142	20	1	A:123-142	20
1.8	ENST00000349736	8	ENSE00000655095	chr20:476446-476363	84	CSK21_HUMAN	143-170	28	1	A:143-170	28
1.9	ENST00000349736	9	ENSE00000655092	chr20:473008-472898	111	CSK21_HUMAN	171-207	37	1	A:171-207	37
1.10	ENST00000349736	10	ENSE00001666435	chr20:470525-470424	102	CSK21_HUMAN	208-241	34	1	A:208-241	34
1.11b	ENST00000349736	11b	ENSE00000655089	chr20:469422-469322	101	CSK21_HUMAN	242-275	34	1	A:242-275	34
1.12	ENST00000349736	12	ENSE00000655088	chr20:468219-468071	149	CSK21_HUMAN	275-325	51	1	A:275-325	51
1.13	ENST00000349736	13	ENSE00000655087	chr20:467106-467020	87	CSK21_HUMAN	325-354	30	1	A:325-329	5
1.14c	ENST00000349736	14c	ENSE00001891680	chr20:464720-461741	2980	CSK21_HUMAN	354-391	38	0	-	-

Asymmetric/Biological 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:327
 aligned with CSK21_HUMAN | P68400 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:327
                                    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       
          CSK21_HUMAN     3 GPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK 329
               SCOP domains d3r0ta_ A: Protein kinase CK2, alpha subunit                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhh.....hhh.eeeeeeeee...eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhh.......eeeeeee....eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee.hhhhhee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------Q--S----------------------------------------------------------------------------------------------------------------------------G----------------------R----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:3-34           -------------------------------------Exon 1.5  PDB: A:72-105           Exon 1.6         Exon 1.7            Exon 1.8  PDB: A:143-170    Exon 1.9  PDB: A:171-207             Exon 1.10  PDB: A:208-241         Exon 1.11b  PDB: A:242-275        -------------------------------------------------1.13  Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.4  PDB: A:34-71 UniProt: 34-71 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:275-325 UniProt: 275-325         ---- Transcript 1 (2)
                 3r0t A   3 GPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK 329
                                    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

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/Biological Unit

Classes(

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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: Protein kinase CK2, alpha subunit (68)

Human (Homo sapiens) [TaxId: 9606] (36)

d3r0ta_

(no "CATH Domain" information available for 3R0T)

(no "Pfam Domain" information available for 3R0T)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CSK21_HUMAN | P68400)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051879	Hsp90 protein binding	Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0019888	protein phosphatase regulator activity	Modulates the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0061077	chaperone-mediated protein folding	The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
	GO:0071174	mitotic spindle checkpoint	A mitotic cell cycle checkpoint that originates from the spindle and delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and oriented, the completion of anaphase until chromosomes are attached to the spindle, or mitotic exit and cytokinesis when the spindle does not form.
	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0030177	positive regulation of Wnt signaling pathway	Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045732	positive regulation of protein catabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016581	NuRD complex	An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
	GO:0031519	PcG protein complex	A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
	GO:0016580	Sin3 complex	A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	3r0t
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3pe1	CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR CX-4945
3pe2	CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR CX-5011

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (2, 2)

Exons (11, 11)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (37, 37)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File