5W89: Human Mcl-1

Crystal structure of human Mcl-1 in complex with modified Bim BH3 peptide SAH-MS1-18. Determined by X-ray diffraction at 1.42 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,458
Mol. weight: 19.88 kDa
Ligands: ZN
Released: 17 Jan 2018

Explore 5W89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W89 contains 9 α-helices and 0 β-strands across 2 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	173-187	15
α-helix	204-223	20
α-helix	225-235	11
α-helix	240-255	16
α-helix	261-280	20
α-helix	284-286	3
α-helix	287-308	22
α-helix	311-318	8

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-19	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Induced myeloid leukemia cell differentiation protein Mcl-1	A	protein	151	Homo sapiens	Q07820 (AlphaFold model)
modified Bim BH3 peptide SAH-MS1-18	B	protein	22	Homo sapiens

Sequence of entity 1 (A), FASTA

>5W89_1 Induced myeloid leukemia cell differentiation protein Mcl-1 (chains A)
GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQG
MLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPL
AESITDVLVRTKRDWLVKQRGWDGFVEFFHV

Sequence of entity 2 (B), FASTA

>5W89_2 modified Bim BH3 peptide SAH-MS1-18 (chains B)
XIWLLQELLRLGDEINARYARX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells. Rezaei Araghi, R., Bird, G.H., Ryan, J.A. et al. Proc Natl Acad Sci U S A (2018) 115:E886-E895. DOI 10.1073/pnas.1712952115 · PubMed

Other PDB entries of the same protein (UniProt Q07820 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VJP 1.13 Å, Histidine-covalent stapled alpha-helical peptide (155H1) targeting hMcl-1
9PQ7 1.24 Å, MBP-Mcl1 in complex with ligand 21b
9PQ5 1.28 Å, MBP-Mcl1 in complex with ligand 8
6UDV 1.35 Å, X-ray co-crystal structure of compound 3 bound to human Mcl-1
9UGP 1.39 Å, Crystal structure of MCL-1 in complex with HRK BH3
8G3S 1.4 Å, MBP-Mcl1 in complex with ligand 11
5C3F 1.43 Å, Crystal structure of Mcl-1 bound to BID-MM
8G3X 1.46 Å, MBP-Mcl1 in complex with ligand 32
8H7B 1.46 Å, The crystal structure of human mcl1 kinase domain in complex with MCL1-M-EBA
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
6OQD 1.48 Å, Crystal structure of Mcl1 with inhibitor 8
5FC4 1.5 Å, Mcl-1 complexed with small molecule inhibitor

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