4QTB - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN ERK1 IN COMPLEX WITH SCH772984 REVEALING A NOVEL INHIBITOR-INDUCED BINDING POCKET

Authors :   A. Chaikuad, T. Keates, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C S. Knapp, Structural Genomics Consortium (Sgc)

Date :   07 Jul 14 (Deposition) - 23 Jul 14 (Release) - 24 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Transferase, Kinase, Mapk, Signalling, Inhibitor, Allosteric, Structural Genomics Consortium (Sgc), Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Chaikuad, E. M C Tacconi, J. Zimmer, Y. Liang, N. S. Gray, M. Tarsounas, S. Knapp
A Unique Inhibitor Binding Site In Erk1/2 Is Associated Wit Slow Binding Kinetics.
Nat. Chem. Biol. V. 10 853 2014
PubMed-ID: 25195011 | Reference-DOI: 10.1038/NCHEMBIO.1629

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 3
	Chains	:	A, B
	EC Number	:	2.7.11.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21-R3-PRARE2
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	KINASE DOMAIN
	Gene	:	ERK1, MAPK3, PRKM3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MAP KINASE 3, MAPK 3, ERT2, EXTRACELLULAR SIGNAL-REGULATED KINASE 1, ERK-1, INSULIN-STIMULATED MAP2 KINASE, MAP KINASE ISOFORM P44, P44-MAPK, MICROTUBULE-ASSOCIATED PROTEIN 2 KINASE, P44-ERK1

		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 (5, 30)

No.	Name	Count	Type	Full Name
1	38Z	2	Ligand/Ion	(3R)-1-(2-OXO-2-{4-[4-(PYRIMIDIN-2-YL)PHENYL]PIPERAZIN-1-YL}ETHYL)-N-[3-(PYRIDIN-4-YL)-2H-INDAZOL-5-YL]PYRROLIDINE-3-CARBOXAMIDE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	20	Ligand/Ion	1,2-ETHANEDIOL
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 17)

No.	Name	Count	Type	Full Name
1	38Z	1	Ligand/Ion	(3R)-1-(2-OXO-2-{4-[4-(PYRIMIDIN-2-YL)PHENYL]PIPERAZIN-1-YL}ETHYL)-N-[3-(PYRIDIN-4-YL)-2H-INDAZOL-5-YL]PYRROLIDINE-3-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	38Z	1	Ligand/Ion	(3R)-1-(2-OXO-2-{4-[4-(PYRIMIDIN-2-YL)PHENYL]PIPERAZIN-1-YL}ETHYL)-N-[3-(PYRIDIN-4-YL)-2H-INDAZOL-5-YL]PYRROLIDINE-3-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:37 , LEU A:107 , HOH A:635	BINDING SITE FOR RESIDUE EDO A 401
02	AC2	SOFTWARE	GLU A:98 , ASN A:99 , GLN A:149 , ARG A:152 , ASP A:179 , HOH A:576	BINDING SITE FOR RESIDUE EDO A 402
03	AC3	SOFTWARE	LEU A:201 , GLU A:203 , TYR A:250 , HOH A:1051	BINDING SITE FOR RESIDUE EDO A 403
04	AC4	SOFTWARE	ARG A:84 , ARG A:87 , GLY A:186 , LEU A:187 , ALA A:188 , ARG A:189 , HOH A:704 , HOH A:926	BINDING SITE FOR RESIDUE EDO A 404
05	AC5	SOFTWARE	TYR A:130 , SER A:170 , EDO A:413 , HOH A:733	BINDING SITE FOR RESIDUE EDO A 405
06	AC6	SOFTWARE	ILE A:190 , ALA A:191 , THR A:347 , PHE A:348 , ALA A:349 , DMS A:415 , HOH A:976	BINDING SITE FOR RESIDUE EDO A 406
07	AC7	SOFTWARE	ASP A:141 , TYR A:145 , TYR A:333 , HOH A:974 , LYS B:289 , VAL B:290 , ALA B:291	BINDING SITE FOR RESIDUE EDO A 407
08	AC8	SOFTWARE	SER A:263 , PRO A:285 , HOH A:595 , HOH A:1008	BINDING SITE FOR RESIDUE EDO A 408
09	AC9	SOFTWARE	SER A:263 , LEU A:281 , GLN A:282 , LEU A:284 , SER A:286 , HOH A:578	BINDING SITE FOR RESIDUE EDO A 409
10	BC1	SOFTWARE	GLU A:323	BINDING SITE FOR RESIDUE EDO A 410
11	BC2	SOFTWARE	PRO A:40 , ARG A:41 , HIS A:62 , VAL A:63 , HOH A:908	BINDING SITE FOR RESIDUE EDO A 411
12	BC3	SOFTWARE	LYS A:65 , LEU A:201 , TYR A:280 , HOH A:911	BINDING SITE FOR RESIDUE EDO A 412
13	BC4	SOFTWARE	ASP A:128 , TYR A:130 , EDO A:405 , HOH A:685 , HOH A:1026	BINDING SITE FOR RESIDUE EDO A 413
14	BC5	SOFTWARE	LEU A:239 , SER A:299 , HOH A:541 , HOH A:731	BINDING SITE FOR RESIDUE DMS A 414
15	BC6	SOFTWARE	ARG A:189 , ILE A:190 , ASP A:192 , PHE A:348 , MET A:350 , EDO A:406 , HOH A:574	BINDING SITE FOR RESIDUE DMS A 415
16	BC7	SOFTWARE	HIS A:197 , ASN A:218 , ILE A:273 , ASN A:274 , ARG B:94	BINDING SITE FOR RESIDUE CL A 416
17	BC8	SOFTWARE	ARG A:208 , ARG A:211 , TYR A:250 , HOH A:936 , HOH A:942 , HOH A:1018 , HOH A:1019 , HOH A:1051	BINDING SITE FOR RESIDUE SO4 A 417
18	BC9	SOFTWARE	ALA A:52 , TYR A:53 , ALA A:69 , LYS A:71 , ILE A:73 , TYR A:81 , ARG A:84 , THR A:85 , GLU A:88 , GLN A:122 , ASP A:123 , MET A:125 , GLU A:126 , THR A:127 , LYS A:131 , LEU A:173 , ASP A:184 , GLY A:186 , HOH A:517 , HOH A:856 , HOH A:1017	BINDING SITE FOR RESIDUE 38Z A 418
19	CC1	SOFTWARE	ARG B:189 , ILE B:190 , ASP B:192 , TYR B:222 , PHE B:348 , HOH B:847	BINDING SITE FOR RESIDUE EDO B 401
20	CC2	SOFTWARE	ARG B:84 , ARG B:87 , GLY B:186 , LEU B:187 , ALA B:188 , ARG B:189 , HOH B:848 , HOH B:981	BINDING SITE FOR RESIDUE EDO B 402
21	CC3	SOFTWARE	TYR B:130 , SER B:170 , HOH B:751	BINDING SITE FOR RESIDUE EDO B 403
22	CC4	SOFTWARE	ASP B:37 , ALA B:109 , HOH B:738 , HOH B:802 , HOH B:807	BINDING SITE FOR RESIDUE EDO B 404
23	CC5	SOFTWARE	SER B:263 , PRO B:285 , HOH B:634	BINDING SITE FOR RESIDUE EDO B 405
24	CC6	SOFTWARE	LEU B:201 , GLU B:203	BINDING SITE FOR RESIDUE EDO B 406
25	CC7	SOFTWARE	LEU B:133 , LYS B:134 , GLU B:237 , ASN B:241 , ARG B:242 , PRO B:243 , HOH B:931	BINDING SITE FOR RESIDUE EDO B 407
26	CC8	SOFTWARE	LEU B:239 , LYS B:298 , SER B:299 , HOH B:610 , HOH B:665 , HOH B:996	BINDING SITE FOR RESIDUE DMS B 408
27	CC9	SOFTWARE	ARG A:94 , HIS B:197 , ASN B:218 , ILE B:273 , ASN B:274	BINDING SITE FOR RESIDUE CL B 409
28	DC1	SOFTWARE	HIS B:78 , GLN B:79	BINDING SITE FOR RESIDUE CL B 410
29	DC2	SOFTWARE	ARG B:208 , ARG B:211 , TYR B:250 , HOH B:521 , HOH B:592 , HOH B:760 , HOH B:960	BINDING SITE FOR RESIDUE SO4 B 411
30	DC3	SOFTWARE	ALA B:52 , TYR B:53 , ALA B:69 , LYS B:71 , ILE B:73 , TYR B:81 , ARG B:84 , THR B:85 , GLU B:88 , GLN B:122 , ASP B:123 , MET B:125 , GLU B:126 , THR B:127 , LYS B:131 , LEU B:173 , ASP B:184 , GLY B:186 , HOH B:541 , HOH B:578 , HOH B:971 , HOH B:972	BINDING SITE FOR RESIDUE 38Z B 412

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

Asymmetric Unit

No.	Residues
1	Gly A:39	-	Pro A:40
2	Gln A:372	-	Pro A:373
3	Gly B:39	-	Pro B:40
4	Gln B:372	-	Pro B:373

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

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

(no "Exon" information available for 4QTB)

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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeeeeeeee..eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh..........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhh.......hhhhhh...hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qtb A  24 VPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPG 374
                                    33        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       303       313       323       333       343       353       363       373

Chain B from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee.....eeeeeeeeee..eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh..........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhh.......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qtb B  27 EVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPG 374
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366

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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gln A:372 - Pro A:373	[ RasMol ]
		Gln B:372 - Pro B:373	[ RasMol ]
		Gly A:39 - Pro A:40	[ RasMol ]
		Gly B:39 - Pro B:40	[ RasMol ]

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	4qtb
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Description

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Ligands, Modified Residues, Ions (5, 30)

Sites (30, 30)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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