2HW6 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MNK1 CATALYTIC DOMAIN

Authors :   R. Jauch, M. C. Wahl

Date :   01 Aug 06 (Deposition) - 29 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Protein Kinase, Drug Design, Mnk1, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Jauch, M. K. Cho, C. Netter, K. Schreiter, B. Aicher, M. Zweckstetter, M. C. Wahl
Mitogen-Activated Protein Kinases Interacting Kinases Are Autoinhibited By A Reprogrammed Activation Segment.
Embo J. V. 25 4020 2006
PubMed-ID: 16917500 | Reference-DOI: 10.1038/SJ.EMBOJ.7601285

Molecule 1 - MAP KINASE-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1
	Chains	:	A, B
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	MNK1-KR
	Gene	:	MKNK1, MNK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MAP KINASE SIGNAL-INTEGRATING KINASE 1, MNK1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:86 , SER A:89 , ARG A:90 , ARG A:93 , HIS B:86 , SER B:89 , ARG B:90 , ARG B:93	BINDING SITE FOR RESIDUE SO4 B 342
2	AC2	SOFTWARE	HIS A:162 , PHE A:236 , LYS A:239 , ARG A:240 , HOH A:363	BINDING SITE FOR RESIDUE SO4 A 342

(no "SS Bond" information available for 2HW6)

(no "Cis Peptide Bond" information available for 2HW6)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040801	K	49	Q	MKNK1_HUMAN	Polymorphism	56351860	A/B	K	49	Q
2	UniProt	VAR_040802	L	158	V	MKNK1_HUMAN	Polymorphism	56408722	A/B	L	158	V

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040801	K	49	Q	MKNK1_HUMAN	Polymorphism	56351860	A	K	49	Q
2	UniProt	VAR_040802	L	158	V	MKNK1_HUMAN	Polymorphism	56408722	A	L	158	V

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040801	K	49	Q	MKNK1_HUMAN	Polymorphism	56351860	B	K	49	Q
2	UniProt	VAR_040802	L	158	V	MKNK1_HUMAN	Polymorphism	56408722	B	L	158	V

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MKNK1_HUMAN	55-78	2	A:55-78 B:55-78
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MKNK1_HUMAN	207-219	2	A:166-178 B:166-178

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MKNK1_HUMAN	55-78	1	A:55-78 -
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MKNK1_HUMAN	207-219	1	A:166-178 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MKNK1_HUMAN	55-78	1	- B:55-78
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MKNK1_HUMAN	207-219	1	- B:166-178

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2l	ENST00000371946	2l	ENSE00001825553	chr1:47069886-47069857	30	MKNK1_HUMAN	-	0	0	-	-
1.4a	ENST00000371946	4a	ENSE00002178389	chr1:47059952-47059785	168	MKNK1_HUMAN	1-12	12	0	-	-
1.9	ENST00000371946	9	ENSE00001708117	chr1:47049001-47048900	102	MKNK1_HUMAN	12-46	35	2	A:39-46 B:40-46	8 7
1.11b	ENST00000371946	11b	ENSE00001645139	chr1:47046299-47046202	98	MKNK1_HUMAN	46-78	33	2	A:46-78 B:46-78	33 33
1.12c	ENST00000371946	12c	ENSE00001660694	chr1:47042326-47042247	80	MKNK1_HUMAN	79-105	27	2	A:79-105 B:79-105	27 27
1.12f	ENST00000371946	12f	ENSE00000957485	chr1:47040692-47040619	74	MKNK1_HUMAN	105-130	26	2	A:105-130 B:105-130	26 26
1.13d	ENST00000371946	13d	ENSE00000957486	chr1:47037839-47037735	105	MKNK1_HUMAN	130-165	36	2	A:130-164 B:130-164	35 35
1.14	ENST00000371946	14	ENSE00000957487	chr1:47037211-47037089	123	MKNK1_HUMAN	165-206	42	2	A:165-165 B:165-165	1 1
1.15b	ENST00000371946	15b	ENSE00002147306	chr1:47034170-47034115	56	MKNK1_HUMAN	206-224	19	2	A:165-183 B:165-183	19 19
1.16b	ENST00000371946	16b	ENSE00000957489	chr1:47030808-47030713	96	MKNK1_HUMAN	225-256	32	2	A:184-196 B:184-196	13 13
1.17d	ENST00000371946	17d	ENSE00000957490	chr1:47028515-47028321	195	MKNK1_HUMAN	257-321	65	2	A:223-260 B:221-260	38 40
1.18c	ENST00000371946	18c	ENSE00001629472	chr1:47027314-47027150	165	MKNK1_HUMAN	322-376	55	2	A:290-335 B:299-334	46 36
1.19	ENST00000371946	19	ENSE00001288731	chr1:47025949-47025906	44	MKNK1_HUMAN	377-391	15	0	-	-
1.20f	ENST00000371946	20f	ENSE00001456524	chr1:47024472-47023090	1383	MKNK1_HUMAN	391-465	75	0	-	-

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:242
 aligned with MKNK1_HUMAN | Q9BUB5 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:338
                                    48        58        68        78        88        98       108       118       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        
          MKNK1_HUMAN    39 SLPGKFEDMYKLTSELLGEGAYAKVQGAVSLQNGKEYAVKIIEKQAGHSRSRVFREVETLYQCQGNKNILELIEFFEDDTRFYLVFEKLQGGSILAHIQKQKHFNEREASRVVRDVAAALDFLHTKDKVSLCHLGWSAMAPSGLTAAPTSLGSSDPPTSASQVAGTTGIAHRDLKPENILCESPEKVSPVKICDFDLGSGMKLNNSCTPITTPELTTPCGSAEYMAPEVVEVFTDQATFYDKRCDLWSLGVVLYIMLSGYPPFVGHCGADCGWDRGEVCRVCQNKLFESIQEGKYEFPDKDWAHISSEAKDLISKLLVRDAKQRLSAAQVLQHPWVQG 376
               SCOP domains d2hw6a_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2hw6A01 A:39-126 Phosphorylase Kinase; domain 1                                         2hw6A02 A:127-335 Transferase(Phosphot                                         ransferase) domain 1                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeeeeeeee...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh-----------------------------------------.......hhh.eee........eee.......--------------------------............hhhhhhhhhhhhhhhhhhhhhh....-----------------------------.....hhhhhh..hhhhhhhhhhhh........hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------Q------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PROTEIN_KINASE_ATP      --------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -------Exon 1.11b  PDB: A:46-78         Exon 1.12c  PDB: A:79-105  ------------------------Exon 1.13d  PDB: A:130-164          ----------------------------------------Exon 1.15b         Exon 1.16b  PDB: A:184-196      Exon 1.17d  PDB: A:223-260 UniProt: 257-321 [INCOMPLETE]         Exon 1.18c  PDB: A:290-335 UniProt: 322-376             Transcript 1 (1)
           Transcript 1 (2) Exon 1.9----------------------------------------------------------Exon 1.12f  PDB: A:105-130----------------------------------Exon 1.14  PDB: A:165-165 UniProt: 165-206-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2hw6 A  39 SLPGKFEDMYKLTSELLGEGAYAKVQGAVSLQNGKEYAVKIIEKQAGHSRSRVFREVETLYQCQGNKNILELIEFFEDDTRFYLVFEKLQGGSILAHIQKQKHFNEREASRVVRDVAAALDFLHTK-----------------------------------------GIAHRDLKPENILCESPEKVSPVKICDFDLGS--------------------------APEVVEVFTDQATFYDKRCDLWSLGVVLYIMLSGYPPF-----------------------------GKYEFPDKDWAHISSEAKDLISKLLVRDAKQRLSAAQVLQHPWVQG 335
                                    48        58        68        78        88        98       108       118       128       138       148       158     |   -         -         -         -       167       177       187        |-         -         -     | 227       237       247       257  |      -         -         -  |    297       307       317       327        
                                                                                                                                                       164                                       165                            196                        223                                  260                           290

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with MKNK1_HUMAN | Q9BUB5 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:336
                                    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       299       309       319       329       339       349       359       369      
          MKNK1_HUMAN    40 LPGKFEDMYKLTSELLGEGAYAKVQGAVSLQNGKEYAVKIIEKQAGHSRSRVFREVETLYQCQGNKNILELIEFFEDDTRFYLVFEKLQGGSILAHIQKQKHFNEREASRVVRDVAAALDFLHTKDKVSLCHLGWSAMAPSGLTAAPTSLGSSDPPTSASQVAGTTGIAHRDLKPENILCESPEKVSPVKICDFDLGSGMKLNNSCTPITTPELTTPCGSAEYMAPEVVEVFTDQATFYDKRCDLWSLGVVLYIMLSGYPPFVGHCGADCGWDRGEVCRVCQNKLFESIQEGKYEFPDKDWAHISSEAKDLISKLLVRDAKQRLSAAQVLQHPWVQ 375
               SCOP domains d2hw6b_ B: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2hw6B01 B:40-126 Phosphorylase Kinase; domain 1                                        2hw6B02 B:127-334 Transferase(Phosphot                                         ransferase) domain 1                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhh.eee.....ee...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhh.........eeeeee...eeeeeee....ee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh-----------------------------------------.......hhh.eee.........ee.......------------------------..............hhhhhhhhhhhhhhhhhhhhhh....--------------------------------------....hhhhhhhhhh..........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------Q------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------PROTEIN_KINASE_ATP      --------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) ------Exon 1.11b  PDB: B:46-78         Exon 1.12c  PDB: B:79-105  ------------------------Exon 1.13d  PDB: B:130-164          ----------------------------------------Exon 1.15b         Exon 1.16b  PDB: B:184-196      Exon 1.17d  PDB: B:221-260 UniProt: 257-321 [INCOMPLETE]         Exon 1.18c  PDB: B:299-334 UniProt: 322-376            Transcript 1 (1)
           Transcript 1 (2) 1.9    ----------------------------------------------------------Exon 1.12f  PDB: B:105-130----------------------------------Exon 1.14  PDB: B:165-165 UniProt: 165-206------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2hw6 B  40 LPGKFEDMYKLTSELLGEGAYAKVQGAVSLQNGKEYAVKIIEKQAGHSRSRVFREVETLYQCQGNKNILELIEFFEDDTRFYLVFEKLQGGSILAHIQKQKHFNEREASRVVRDVAAALDFLHTK-----------------------------------------GIAHRDLKPENILCESPEKVSPVKICDFDLGS------------------------YMAPEVVEVFTDQATFYDKRCDLWSLGVVLYIMLSGYPPF--------------------------------------WAHISSEAKDLISKLLVRDAKQRLSAAQVLQHPWVQ 334
                                    49        59        69        79        89        99       109       119       129       139       149       159    |    -         -         -         -      |168       178       188       | -         -         -  |    228       238       248       258 |       -         -         -         -|      308       318       328      
                                                                                                                                                      164                                       165                            196                      221                                    260                                    299

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(

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Folds(

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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: automated matches (529)

Protein domain: automated matches (529)

Human (Homo sapiens) [TaxId: 9606] (438)

1a	d2hw6a_	A:
1b	d2hw6b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

1a	2hw6A01	A:39-126
1b	2hw6B01	B:40-126

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

2a	2hw6A02	A:127-335
2b	2hw6B02	B:127-334

(no "Pfam Domain" information available for 2HW6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MKNK1_HUMAN | Q9BUB5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0009931	calcium-dependent protein serine/threonine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0004683	calmodulin-dependent protein kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
	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: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: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:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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: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:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006446	regulation of translational initiation	Any process that modulates the frequency, rate or extent of translational initiation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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	2hw6
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	MKNK1_HUMAN \| Q9BUB5
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	2.7.11.1
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	MKNK1_HUMAN \| Q9BUB5
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UniProtKB/Swiss-Prot
	MKNK1_HUMAN \| Q9BUB5	:	2y9q

2ac3	2AC3 IS THE CRYSTAL STRUCTURE OF HUMAN MNK2 KINASE DOMAIN AT 2.10 ANGSTROM RESOLUTION
2ac5	2AC5 IS THE CRYSTAL STRUCTURE OF HUMAN MNK2 KINASE DOMAIN D228G MUTANT AT 3.20 ANGSTROM RESOLUTION
2hw7	2HW7 IS THE CRYSTAL STRUCTURE OF HUMAN MNK2 KINASE DOMAIN D228G MUTANT IN COMPLEX WITH STAUROSPORINE AT 2.71 ANGSTROM RESOLUTION

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Gene Ontology (21, 21)

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