6DM8: PDB entry 6DM8

Understanding the Species Selectivity of Myeloid cell leukemia-1 (Mcl-1) inhibitors. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Escherichia coli (strain K12), Mus musculus
Chains: 8
Atoms: 32,595
Mol. weight: 479.37 kDa
Ligands: 6AK
Released: 1 Aug 2018

Explore 6DM8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DM8 contains 258 α-helices and 188 β-strands across 8 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: 35 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	-212	1
β-strand	-209--205	5	1
α-helix	-198--184	15
β-strand	-181--177	5	1
α-helix	-172--163	10
β-strand	-156--152	5	1
α-helix	-151--149	3
α-helix	-148--143	6
β-strand	-139	1	2
α-helix	-138--136	3
α-helix	-132--129	4
β-strand	-126	1	3
α-helix	-124--120	5
β-strand	-117--116	2	4
β-strand	-113--112	2	4
β-strand	-110--104	7	1
β-strand	-101--97	5	5
β-strand	-87	1	6
α-helix	-83--74	10
β-strand	-70--68	3	5
α-helix	-61--59	3
α-helix	-57--54	4
β-strand	-48--46	3	7
β-strand	-34--33	2	7
α-helix	-29--15	15
α-helix	-5-3	9
β-strand	7-12	6	5
α-helix	14-16	3
α-helix	17-22	6
β-strand	27-30	4	5
α-helix	31-33	3
β-strand	34-35	2	6
β-strand	38-39	2	6
α-helix	40	1
α-helix	42	1
β-strand	43-44	2	8
β-strand	45-51	7	1
β-strand	52	1	2
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	1
β-strand	89	1	3
α-helix	90-96	7
α-helix	100-110	11
β-strand	113-114	2	8
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-153	12
α-helix	155-172	18
α-helix	185-204	20
α-helix	206-213	8
α-helix	221-225	5
α-helix	227-236	10
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	293-300	8

Chain B: 35 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	-211	1
β-strand	-207--204	4	9
α-helix	-197--183	15
β-strand	-179--176	4	9
α-helix	-171--162	10
β-strand	-155--151	5	9
α-helix	-150--148	3
α-helix	-147--142	6
β-strand	-138	1	10
α-helix	-137--135	3
α-helix	-131--128	4
β-strand	-125	1	11
α-helix	-123--118	6
β-strand	-116--115	2	12
β-strand	-112--111	2	12
β-strand	-109--103	7	9
β-strand	-100--96	5	13
β-strand	-86	1	14
α-helix	-82--73	10
β-strand	-69--67	3	13
α-helix	-60--58	3
α-helix	-56--53	4
β-strand	-47--45	3	15
β-strand	-34--33	2	15
α-helix	-29--15	15
α-helix	-5-3	9
β-strand	7-12	6	13
α-helix	14-16	3
α-helix	17-23	7
β-strand	27-30	4	13
α-helix	31-33	3
β-strand	34	1	14
β-strand	35	1	16
β-strand	38	1	16
α-helix	39-40	2
α-helix	42	1
β-strand	43-44	2	17
β-strand	45-51	7	9
β-strand	52	1	10
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	9
β-strand	89	1	11
α-helix	90-96	7
α-helix	100-111	12
β-strand	113-114	2	17
α-helix	115-116	2
α-helix	121-136	16
α-helix	142-153	12
α-helix	155-172	18
α-helix	184-204	21
α-helix	211-214	4
α-helix	221-226	6
α-helix	228-236	9
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	292-300	9

Chain C: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	-211	1
β-strand	-207--204	4	18
α-helix	-197--183	15
β-strand	-179--176	4	18
α-helix	-171--163	9
β-strand	-155--151	5	18
α-helix	-150--148	3
α-helix	-147--142	6
β-strand	-138	1	19
α-helix	-137--135	3
α-helix	-131--128	4
β-strand	-125	1	20
α-helix	-123--118	6
β-strand	-116--115	2	21
β-strand	-112--111	2	21
β-strand	-108--103	6	18
β-strand	-100--96	5	22
β-strand	-86	1	23
α-helix	-82--74	9
β-strand	-69--67	3	22
α-helix	-56--53	4
β-strand	-47--44	4	24
β-strand	-38--33	6	24
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	22
α-helix	14-16	3
α-helix	17-23	7
β-strand	27-30	4	22
α-helix	31-33	3
β-strand	34	1	23
β-strand	35	1	25
β-strand	38	1	25
α-helix	42	1
β-strand	43-44	2	26
β-strand	45-51	7	18
β-strand	52	1	19
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	18
β-strand	89	1	20
α-helix	90-96	7
α-helix	100-111	12
β-strand	113-114	2	26
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-172	31
α-helix	184-204	21
α-helix	207-215	9
α-helix	221-236	16
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	292-299	8

Chain D: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	-209--205	5	27
α-helix	-198--184	15
β-strand	-181--177	5	27
α-helix	-172--164	9
β-strand	-156--152	5	27
α-helix	-151--149	3
α-helix	-148--143	6
β-strand	-139	1	28
α-helix	-138--136	3
α-helix	-132--129	4
β-strand	-126	1	29
α-helix	-124--120	5
β-strand	-117--116	2	30
β-strand	-113--112	2	30
β-strand	-109--104	6	27
β-strand	-101--97	5	31
β-strand	-87	1	32
α-helix	-84--75	10
β-strand	-70--68	3	31
α-helix	-61--54	8
β-strand	-46--45	2	33
α-helix	-43--41	3
β-strand	-38--37	2	33
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	31
α-helix	14-16	3
α-helix	17-22	6
β-strand	27-30	4	31
α-helix	31-33	3
β-strand	34-35	2	32
β-strand	38-39	2	32
α-helix	40	1
β-strand	43-44	2	34
β-strand	45-51	7	27
β-strand	52	1	28
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	27
β-strand	89	1	29
α-helix	90-96	7
α-helix	100-110	11
β-strand	113-114	2	34
α-helix	121-137	17
α-helix	142-172	31
α-helix	187-204	18
α-helix	206-215	10
α-helix	221-225	5
α-helix	227-234	8
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	292-300	9

Chain E: 33 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	-212	1
β-strand	-208--205	4	35
α-helix	-198--184	15
β-strand	-180--177	4	35
α-helix	-172--163	10
β-strand	-156--152	5	35
α-helix	-151--149	3
α-helix	-148--143	6
β-strand	-139--138	2	35
α-helix	-137--136	2
α-helix	-132--129	4
β-strand	-126	1	36
α-helix	-124--120	5
β-strand	-117--116	2	37
β-strand	-113--112	2	37
β-strand	-110--104	7	35
β-strand	-101--97	5	38
β-strand	-87	1	39
α-helix	-83--75	9
β-strand	-70--68	3	38
α-helix	-57--54	4
β-strand	-48--46	3	40
β-strand	-34--33	2	40
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	38
α-helix	14-16	3
α-helix	17-23	7
β-strand	27-30	4	38
α-helix	31-33	3
β-strand	34-35	2	39
β-strand	38-39	2	39
α-helix	40	1
α-helix	42	1
β-strand	43-44	2	41
β-strand	45-52	8	35
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	35
β-strand	89	1	36
α-helix	90-96	7
α-helix	100-111	12
β-strand	113-114	2	41
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-153	12
α-helix	155-172	18
α-helix	185-204	20
α-helix	206-209	4
α-helix	221-236	16
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	293-300	8

Chain F: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	-208--205	4	42
α-helix	-198--184	15
β-strand	-180--177	4	42
α-helix	-172--164	9
β-strand	-156--152	5	42
α-helix	-151--149	3
α-helix	-148--143	6
β-strand	-139	1	43
α-helix	-138--136	3
α-helix	-132--129	4
β-strand	-126	1	44
α-helix	-124--120	5
β-strand	-117--116	2	45
β-strand	-113--112	2	45
β-strand	-109--104	6	42
β-strand	-101--97	5	46
β-strand	-87	1	47
α-helix	-83--75	9
β-strand	-70--68	3	46
α-helix	-61--54	8
β-strand	-46--45	2	48
β-strand	-38--37	2	48
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	46
α-helix	14-16	3
α-helix	17-22	6
β-strand	27-30	4	46
α-helix	31-33	3
β-strand	34	1	47
β-strand	35	1	49
β-strand	38	1	49
α-helix	39-40	2
β-strand	43-44	2	50
β-strand	45-51	7	42
β-strand	52	1	43
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	42
β-strand	89	1	44
α-helix	90-96	7
α-helix	100-110	11
β-strand	113-114	2	50
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-172	31
α-helix	187-199	13
α-helix	206-215	10
α-helix	221-225	5
α-helix	227-235	9
α-helix	242-261	20
α-helix	265-267	3
α-helix	268-289	22
α-helix	292-299	8

Chain G: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	-211	1	51
β-strand	-209--205	5	51
α-helix	-198--184	15
β-strand	-181--177	5	51
α-helix	-172--164	9
β-strand	-156--152	5	51
α-helix	-151--149	3
α-helix	-148--143	6
β-strand	-139	1	52
α-helix	-138--136	3
α-helix	-132--129	4
β-strand	-126	1	53
α-helix	-124--120	5
β-strand	-117--116	2	54
β-strand	-113--112	2	54
β-strand	-109--104	6	51
β-strand	-101--97	5	55
β-strand	-87	1	56
α-helix	-83--75	9
β-strand	-70--68	3	55
α-helix	-61--54	8
β-strand	-45--44	2	57
β-strand	-39--38	2	57
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	55
α-helix	14-16	3
α-helix	17-22	6
β-strand	27-30	4	55
α-helix	31-33	3
β-strand	34	1	56
β-strand	35	1	58
β-strand	38	1	58
α-helix	39-40	2
β-strand	43-44	2	59
β-strand	45-51	7	51
β-strand	52	1	52
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	51
β-strand	89	1	53
α-helix	90-96	7
α-helix	100-110	11
β-strand	113-114	2	59
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-172	31
α-helix	185-200	16
α-helix	206-211	6
α-helix	221-225	5
α-helix	227-235	9
α-helix	242-261	20
α-helix	268-289	22
α-helix	292-299	8

Chain H: 32 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	-207--204	4	60
α-helix	-197--183	15
β-strand	-179--176	4	60
α-helix	-171--162	10
β-strand	-155--151	5	60
α-helix	-150--148	3
α-helix	-147--141	7
β-strand	-138	1	61
α-helix	-137--135	3
α-helix	-131--128	4
β-strand	-125	1	62
α-helix	-123--119	5
β-strand	-116--115	2	63
β-strand	-112--111	2	63
β-strand	-109--103	7	60
β-strand	-100--96	5	64
β-strand	-86	1	65
α-helix	-85--83	3
α-helix	-82--73	10
β-strand	-69--67	3	64
α-helix	-60--53	8
β-strand	-44--43	2	66
β-strand	-38--37	2	66
α-helix	-29--15	15
α-helix	-5-4	10
β-strand	7-12	6	64
α-helix	14-16	3
α-helix	17-22	6
β-strand	27-30	4	64
α-helix	31-33	3
β-strand	34-35	2	65
β-strand	38-39	2	65
α-helix	40	1
β-strand	43-44	2	67
β-strand	45-51	7	60
β-strand	52	1	61
α-helix	58-64	7
α-helix	65-69	5
α-helix	72-81	10
β-strand	86-87	2	60
β-strand	89	1	62
α-helix	90-96	7
α-helix	100-110	11
β-strand	113-114	2	67
α-helix	115-116	2
α-helix	121-137	17
α-helix	142-171	30
α-helix	184-192	9
α-helix	198-204	7
α-helix	206-212	7
α-helix	224-233	10
α-helix	239-258	20
α-helix	262-264	3
α-helix	265-286	22
α-helix	289-296	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera	A, B, C, D, E, F, G, H	protein	518	Escherichia coli (strain K12), Mus musculus	P0AEX9 (AlphaFold model), P97287 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>6DM8_1 Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera (chains A, B, C, D, E, F, G, H)
GKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDE
ALKDAQTGSDLYRQSLEIISRYLREQATGSKDSKPLGEAGAAGRRALETLRRVGDGVQRN
HETAFQGMLRKLDIKNEGDVKSFSRVMVHVFKDGVTNWGRIVTLISFGAFVAKHLKSVNQ
ESFIEPLAETITDVLVRTKRDWLVKQRGWDGFVEFFHV

Ligands and cofactors

ID	Name	Formula	Copies
6AK	4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethy…	C39 H39 Cl2 N5 O4	24

Primary citation

Understanding the Species Selectivity of Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors. Zhao, B., Arnold, A.L., Coronel, M.A. et al. Biochemistry (2018) 57:4952-4958. DOI 10.1021/acs.biochem.8b00626 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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