4IC7: ERK5 kinase domain

Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,394
Mol. weight: 128.99 kDa
Ligands: ANP
Released: 13 Feb 2013

Explore 4IC7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IC7 contains 55 α-helices and 37 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	1
β-strand	63	1	1
β-strand	68-74	7	1
β-strand	80-86	7	1
α-helix	93-108	16
β-strand	114	1	2
β-strand	117-120	4	1
α-helix	121-123	3
β-strand	133-138	6	1
β-strand	142-143	2	2
α-helix	144-148	5
α-helix	156-175	20
β-strand	178-179	2	3
α-helix	185-187	3
β-strand	188-190	3	2
β-strand	196-198	3	2
β-strand	205-206	2	3
α-helix	216-218	3
α-helix	230-234	5
α-helix	242-257	16
α-helix	267-278	12
α-helix	281-282	2
α-helix	283-286	4
α-helix	295-298	4
α-helix	306-308	3
α-helix	309-312	4
α-helix	318-327	10
α-helix	332-334	3
α-helix	336-337	2
α-helix	338-341	4
α-helix	345-347	3
α-helix	353-355	3
α-helix	362-363	2
α-helix	374-383	10
α-helix	386-390	5
β-strand	396-398	3	4

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	4
β-strand	27-32	6	4
α-helix	41-51	11
β-strand	60-63	4	9
β-strand	69-72	4	9
α-helix	77-94	18
α-helix	97-101	5
β-strand	102-104	3	4
β-strand	105-106	2	9
α-helix	107-108	2

Chain D: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	5
β-strand	63	1	5
β-strand	68-74	7	5
β-strand	80-87	8	5
α-helix	93-96	4
α-helix	99-108	10
β-strand	114	1	6
β-strand	117-120	4	5
β-strand	132-137	6	5
β-strand	142-143	2	6
α-helix	144-148	5
α-helix	156-175	20
β-strand	179	1	7
α-helix	185-187	3
β-strand	188-190	3	6
β-strand	196-198	3	6
β-strand	205	1	7
α-helix	211-213	3
α-helix	230-233	4
α-helix	242-257	16
α-helix	267-277	11
α-helix	281-282	2
α-helix	283-287	5
α-helix	295-298	4
α-helix	302-303	2
α-helix	305-308	4
α-helix	309-312	4
α-helix	318-327	10
α-helix	332-334	3
α-helix	336-337	2
α-helix	338-341	4
α-helix	345-347	3
α-helix	353-355	3
α-helix	366-371	6
α-helix	377-383	7
α-helix	386-391	6
β-strand	398	1	8

Chain E: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	8
β-strand	27-33	7	8
α-helix	41-51	11
β-strand	60-63	4	8
β-strand	69-72	4	8
α-helix	77-94	18
α-helix	99-101	3
β-strand	102-106	5	8
α-helix	107-110	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 7	A, D	protein	442	Homo sapiens	Q13164 (AlphaFold model)
Dual specificity mitogen-activated protein kinase kinase 5	B, E	protein	126	Homo sapiens	Q13163 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4IC7_1 Mitogen-activated protein kinase 7 (chains A, D)
GSMAEPLKEEDGEDGSAEPPGPVKAEPAHTAASVAAKNLALLKARSFDVTFDVGDEYEII
ETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIK
DILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQV
IHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHE
YTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYI
QSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPD
CAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGIRQQIRFQPSLQPVASEPGCPDVE
MPSPWAPSGDCAMSGRHHHHHH

Sequence of entity 2 (B, E), FASTA

>4IC7_2 Dual specificity mitogen-activated protein kinase kinase 5 (chains B, E)
GSVLVIRIKIPNSGAVDWTVHSGPQLLFRDVLDVIGQVLPEATTTAFEYEDEDGDRITVR
SDEEMKAMLSYYYSTVMEQQVNGQLIEPLQIFPRACKPPGERNIHGLKVNTRAGPSQSGR
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Structural mechanism for the specific assembly and activation of the extracellular signal regulated kinase 5 (ERK5) module. Glatz, G., Gogl, G., Alexa, A. et al. J Biol Chem (2013) 288:8596-8609. DOI 10.1074/jbc.M113.452235 · PubMed

Other PDB entries of the same protein (UniProt Q13164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BYZ 1.65 Å, ERK5 in complex with small molecule
4ZSG 1.79 Å, Mitogen activated protein kinase 7 in complex with inhibitor
2Q8Y 2.0 Å, Structural insight into the enzymatic mechanism of the phophothreonine lyase
4ZSL 2.25 Å, Mitogen activated protein kinase 7 in complex with inhibitor
6HKN 2.33 Å, Crystal structure of Compound 35 with ERK5
9LTA 2.33 Å, Crystal Structure of Compound SKLB-D18 with MAPK7 (ERK5)
5O7I 2.38 Å, ERK5 in complex with a pyrrole inhibitor
6HKM 2.47 Å, Crystal structure of Compound 1 with ERK5
4ZSJ 2.48 Å, Mitogen activated protein kinase 7 in complex with inhibitor
7PUS 2.59 Å, ERK5 in complex with Pyrrole Carboxamide scaffold
5BYY 2.79 Å, ERK5 in complex with small molecule
4B99 2.8 Å, Crystal Structure of MAPK7 (ERK5) with inhibitor

Browse structure collections

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