5MEV: MCL1 FAB complex

MCL1 FAB complex in complex with compound 21. Determined by X-ray diffraction at 2.94 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 2.94 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,488
Mol. weight: 67.63 kDa
Ligands: 7LW
Released: 18 Jan 2017

Explore 5MEV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MEV contains 23 α-helices and 52 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	173-191	19
α-helix	198-199	2
α-helix	204-223	20
α-helix	225-234	10
α-helix	240-244	5
α-helix	247-250	4
α-helix	251-253	3
α-helix	261-280	20
α-helix	288-299	12
α-helix	303-308	6
α-helix	311-319	9

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	106-109	4	3
β-strand	113-115	3	3
β-strand	116-117	2	2
α-helix	123-125	3
β-strand	126-130	5	4
β-strand	142-151	10	4
β-strand	157-160	4	5
α-helix	161-163	3
β-strand	165	1	5
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-177	3	4
β-strand	180-189	10	4
β-strand	199-205	7	5
β-strand	210-216	7	5

Chain L: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5	1	7
β-strand	11-12	2	8
β-strand	19-20	2	9
β-strand	23	1	7
β-strand	35-39	5	10
α-helix	44-45	2
β-strand	46-49	4	10
β-strand	50	1	11
β-strand	54	1	11
β-strand	64-65	2	9
β-strand	74-75	2	9
β-strand	86-93	8	10
β-strand	98-101	4	10
β-strand	102	1	6
β-strand	105-106	2	10
β-strand	108-109	2	8
α-helix	113-114	2
β-strand	115	1	12
β-strand	118-122	5	13
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	13
β-strand	144	1	12
β-strand	149-151	3	14
β-strand	153-154	2	15
β-strand	157-158	2	15
α-helix	159	1
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-170	2	13
β-strand	176-185	10	13
α-helix	186-190	5
β-strand	194-195	2	15
β-strand	198-201	4	14
β-strand	204-207	4	14
β-strand	210-211	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell…	A	protein	162	Mus musculus, Homo sapiens	P97287 (AlphaFold model), Q07820 (AlphaFold model)
Fab Heavy Chain	H	protein	230	Homo sapiens
Fab Light Chain	L	protein	226	Homo sapiens

Sequence of entity 1 (A), FASTA

>5MEV_1 Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1 (chains A)
GPLGSEDDLYRQSLEIISRYLREQATGSKDSKPLGEAGAAGRRALETLRRVGDGVQRNHE
TAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQES
CIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVEDLEGG

Sequence of entity 2 (H), FASTA

>5MEV_2 Fab Heavy Chain (chains H)
QVTLKESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYIYY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARQVGATWAFDIWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCAAAENLYFQ

Sequence of entity 3 (L), FASTA

>5MEV_3 Fab Light Chain (chains L)
QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVP
DRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNAWVFGGGTKLTVLGQPKSSPSVT
LFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASS
YLTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCAAAENLYFQGS

Ligands and cofactors

ID	Name	Formula	Copies
7LW	(5~{R},13~{S},17~{S})-5-[(3,4-dichlorophenyl)methyl]-8-methyl-13-[(4-methylsulf…	C37 H43 Cl2 N5 O6 S	1

Primary citation

Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors. Johannes, J.W., Bates, S., Beigie, C. et al. ACS Med Chem Lett (2017) 8:239-244. DOI 10.1021/acsmedchemlett.6b00464 · PubMed

Other PDB entries of the same protein (UniProt P97287 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NL9 1.55 Å, Crystal structure of the Mcl-1:Bim BH3 complex
4BPJ 1.6 Å, Mcl-1 bound to alpha beta Puma BH3 peptide 3
5VX2 1.85 Å, Mcl-1 in complex with Bim-h3Pc-RT
4BPI 1.98 Å, Mcl-1 bound to alpha beta Puma BH3 peptide 2
4G35 2.0 Å, Mcl-1 in complex with a biphenyl cross-linked Noxa peptide.
3D7V 2.03 Å, Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3 ligand
5KU9 2.2 Å, Crystal structure of MCL1 with compound 1
5MES 2.24 Å, MCL1 FAB complex in complex with compound 29
3IO9 2.4 Å, BimL12Y in complex with Mcl-1
6DM8 2.7 Å, Understanding the Species Selectivity of Myeloid cell leukemia-1 (Mcl-1) inhibitors
2NLA 2.8 Å, Crystal structure of the Mcl-1:mNoxaB BH3 complex
1WSX Solution structure of MCL-1

Browse structure collections

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