3VVH: Human mitogen-activated protein kinase kinase 1

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP. Determined by X-ray diffraction at 2.0 Å resolution. Released 28 Aug 2013.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,168
Mol. weight: 116.83 kDa
Ligands: MG, ATP, 4BM
Released: 28 Aug 2013

Explore 3VVH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VVH contains 57 α-helices and 30 β-strands across 3 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
β-strand	68-76	9	1
β-strand	80-87	8	1
β-strand	92	1	2
β-strand	93-100	8	1
α-helix	105-115	11
α-helix	116-120	5
β-strand	126	1	3
β-strand	129-135	7	1
β-strand	138-144	7	1
β-strand	150	1	3
α-helix	151-158	8
α-helix	163-184	22
α-helix	193-195	3
β-strand	196-198	3	3
β-strand	204-206	3	3
α-helix	213-219	7
α-helix	232-235	4
α-helix	243-258	16
α-helix	265-266	2
α-helix	269-274	6
α-helix	307-309	3
α-helix	310-319	10
α-helix	321-323	3
α-helix	332-341	10
α-helix	350-351	2
α-helix	352-356	5
α-helix	359-366	8
β-strand	369	1	4
α-helix	371-379	9

Chain B: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
β-strand	68-76	9	4
β-strand	80-87	8	4
β-strand	92-100	9	4
α-helix	105-115	11
α-helix	116-120	5
β-strand	126	1	5
β-strand	129-135	7	4
β-strand	138-144	7	4
β-strand	150	1	5
α-helix	151-158	8
α-helix	163-184	22
α-helix	193-195	3
β-strand	196-198	3	5
β-strand	204-206	3	5
α-helix	213-219	7
α-helix	221-223	3
α-helix	234-236	3
α-helix	238-240	3
α-helix	242-258	17
α-helix	265-267	3
α-helix	268-274	7
α-helix	310-319	10
α-helix	321-323	3
α-helix	325-326	2
α-helix	332-341	10
α-helix	352-356	5
α-helix	359-366	8
α-helix	371-379	9

Chain C: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
β-strand	68-76	9	6
β-strand	80-87	8	6
β-strand	92-100	9	6
α-helix	105-115	11
α-helix	116-120	5
β-strand	126	1	7
β-strand	129-135	7	6
β-strand	138-144	7	6
β-strand	150	1	7
α-helix	151-158	8
α-helix	163-184	22
α-helix	193-195	3
β-strand	196-198	3	7
β-strand	204-206	3	7
α-helix	213-219	7
α-helix	221-223	3
α-helix	234-236	3
α-helix	238-240	3
α-helix	242-258	17
α-helix	265-266	2
α-helix	310-319	10
α-helix	321-323	3
α-helix	332-341	10
α-helix	352-356	5
α-helix	359-366	8
β-strand	369	1	2
α-helix	371-379	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dual specificity mitogen-activated protein kinase kinase 1	A, B, C	protein	341	Homo sapiens	Q02750 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3VVH_1 Dual specificity mitogen-activated protein kinase kinase 1 (chains A, B, C)
MELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHE
CNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYL
REKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHY
SVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLSSY
GMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAF
IKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGVLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
4BM	N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]…	C16 H14 F3 I N2 O4	3

Primary citation

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP. Kudo, N., Kato, R., Wakatsuki, S. To be published.

Other PDB entries of the same protein (UniProt Q02750 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7B7R 1.7 Å, MEK1 in complex with compound 4
7B9L 1.7 Å, MEK1 in complex with compound 23
3EQC 1.8 Å, X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a…
3EQI 1.9 Å, X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a…
3EQH 2.0 Å, X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a…
7B94 2.0 Å, MEK1 in complex with compound 6
7F2X 2.01 Å, Crystal structure of MEK1 C121S mutant
9AXX 2.07 Å, Crystal structure of BRAF/MEK1 complex with NST-628 and an active RAF dimer
3EQD 2.1 Å, X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a…
4AN3 2.1 Å, Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518…
7XLP 2.1 Å, MEK1 bound to DS03090629
7XNC 2.1 Å, MEK1 bound to DS94070624

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