5MES: MCL1 FAB complex

MCL1 FAB complex in complex with compound 29. Determined by X-ray diffraction at 2.24 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 2.24 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,679
Mol. weight: 67.66 kDa
Ligands: 7LT
Released: 18 Jan 2017

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

Secondary structure: helices and β-sheets

5MES contains 26 α-helices and 48 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	204-223	20
α-helix	225-235	11
α-helix	240-245	6
α-helix	247-250	4
α-helix	251-253	3
α-helix	261-280	20
α-helix	284-286	3
α-helix	287-301	15
α-helix	303-308	6
α-helix	311-319	9

Chain H: 8 helices, 23 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
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
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	121-122	2
β-strand	123	1	4
β-strand	126-130	5	5
β-strand	142-151	10	5
β-strand	152	1	4
β-strand	157-160	4	6
α-helix	161-163	3
β-strand	165	1	6
β-strand	169-171	3	5
α-helix	172-174	3
β-strand	175-177	3	5
β-strand	180-189	10	5
β-strand	200-205	6	6
α-helix	206-208	3
β-strand	210-215	6	6

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	5	1	8
β-strand	9-12	4	9
β-strand	18-23	6	8
β-strand	35-39	5	9
β-strand	46-49	4	9
β-strand	50	1	10
β-strand	54	1	10
β-strand	63-68	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-93	9	9
β-strand	98-101	4	9
β-strand	102	1	7
β-strand	105-109	5	9
α-helix	113-114	2
β-strand	115	1	11
β-strand	118-122	5	12
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	12
β-strand	144	1	11
β-strand	149-154	6	13
β-strand	157-158	2	13
α-helix	159	1
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
α-helix	186-191	6
β-strand	194-200	7	13
β-strand	207-213	7	13

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)
Heavy Chain	H	protein	230	Homo sapiens
Light Chain	L	protein	226	Homo sapiens

Sequence of entity 1 (A), FASTA

>5MES_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

>5MES_2 Heavy Chain (chains H)
QVTLKESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYIYY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARQVGATWAFDIWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCAAAENLYFQ

Sequence of entity 3 (L), FASTA

>5MES_3 Light Chain (chains L)
QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVP
DRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNAWVFGGGTKLTVLGQPKSSPSVT
LFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASS
YLTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCAAAENLYFQGS

Ligands and cofactors

ID	Name	Formula	Copies
7LT	(5~{R},13~{S},17~{S})-5-[[4-chloranyl-3-(2-phenylethyl)phenyl]methyl]-13-[(4-ch…	C44 H49 Cl2 N5 O4	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
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
5MEV 2.94 Å, MCL1 FAB complex in complex with compound 21
1WSX Solution structure of MCL-1

Browse structure collections

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