6DM8 | pdb_00006dm8

Understanding the Species Selectivity of Myeloid cell leukemia-1 (Mcl-1) inhibitors

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8043136	3001974	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Bcl-2	e6dm8H3	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
H	SBP_bac_1_C	e6dm8H2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
G	Bcl-2	e6dm8G1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
G	SBP_bac_1_C	e6dm8G3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
F	Bcl-2	e6dm8F1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
F	SBP_bac_1_C	e6dm8F3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
E	Bcl-2	e6dm8E3	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
E	SBP_bac_1_C	e6dm8E2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
D	Bcl-2	e6dm8D1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
D	SBP_bac_1_C	e6dm8D2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
C	Bcl-2	e6dm8C2	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
C	SBP_bac_1_C	e6dm8C1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B	Bcl-2	e6dm8B2	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
B	SBP_bac_1_C	e6dm8B1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A	Bcl-2	e6dm8A3	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2	ECOD (1.6)
A	SBP_bac_1_C	e6dm8A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
H	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
G	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
G	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
F	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
F	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
E	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
D	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
A	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	PF00452	Apoptosis regulator proteins, Bcl-2 family (Bcl-2)	Apoptosis regulator proteins, Bcl-2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein heterodimerization activity protein binding protein dimerization activity death domain binding BH3 domain binding BH domain binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein heterodimerization activity protein binding protein dimerization activity death domain binding BH3 domain binding BH domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus positive regulation of cell communication intrinsic apoptotic signaling pathway in response to oxidative stress neuron apoptotic process regulation of cellular process positive regulation of signal transduction regulation of oxidative stress-induced intrinsic apoptotic signaling pathway signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction signal transduction intrinsic apoptotic signaling pathway positive regulation of neuron apoptotic process positive regulation of cellular process regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation positive regulation of intracellular signal transduction cell death positive regulation of apoptotic process neuron intrinsic apoptotic signaling pathway in response to oxidative stress apoptotic signaling pathway regulation of response to stimulus positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway apoptotic process programmed cell death regulation of neuron apoptotic process regulation of apoptotic signaling pathway positive regulation of signaling developmental process cellular developmental process cell differentiation cellular component organization organelle organization apoptotic mitochondrial changes cellular component organization or biogenesis mitochondrion organization negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling negative regulation of biological process negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of anoikis negative regulation of anoikis anoikis response to peptide response to cytokine intrinsic apoptotic signaling pathway in response to DNA damage negative regulation of catabolic process catabolic process negative regulation of metabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol Bcl-2 family protein complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020726	Apoptosis regulator, Bcl-2, BH2 motif, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036834	Bcl-2-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR046371	Bcl-2, Bcl-2 homology region 1-3	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002475	Bcl2-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR026298	Bcl-2 family	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020717	Apoptosis regulator, Bcl-2, BH1 motif, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013281	Apoptosis regulator, Mcl-1	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020728	Apoptosis regulator, Bcl-2, BH3 motif, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.