7NPR | pdb_00007npr

Structure of an intact ESX-5 inner membrane complex, Composite C3 model

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
Z [auth P2]	AAA_lid_RFC1	e7nprP21	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
Y [auth P1]	AAA_lid_RFC1	e7nprP11	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
AA [auth P3]	AAA_lid_RFC1	e7nprP31	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
X [auth DC]	AAA_lid_RFC1	e7nprDC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
W [auth DB]	AAA_lid_RFC1	e7nprDB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
V [auth DA]	AAA_lid_RFC1	e7nprDA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
U [auth D9]	AAA_lid_RFC1	e7nprD91	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
T [auth D8]	AAA_lid_RFC1	e7nprD81	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
S [auth D7]	AAA_lid_RFC1	e7nprD71	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
R [auth D6]	AAA_lid_RFC1	e7nprD61	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
Q [auth D5]	AAA_lid_RFC1	e7nprD51	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
P [auth D4]	AAA_lid_RFC1	e7nprD41	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
O [auth D3]	AAA_lid_RFC1	e7nprD31	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
N [auth D2]	AAA_lid_RFC1	e7nprD21	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
M [auth D1]	AAA_lid_RFC1	e7nprD11	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
L [auth C6]	AAA_lid_RFC1	e7nprC61	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
K [auth C5]	AAA_lid_RFC1	e7nprC51	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
J [auth C4]	AAA_lid_RFC1	e7nprC41	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
I [auth C3]	AAA_lid_RFC1	e7nprC31	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
H [auth C2]	AAA_lid_RFC1	e7nprC21	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
G [auth C1]	AAA_lid_RFC1	e7nprC11	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
F [auth B6]	AAA_lid_RFC1	e7nprB61	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
E [auth B5]	AAA_lid_RFC1	e7nprB51	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
D [auth B4]	AAA_lid_RFC1	e7nprB41	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
C [auth B3]	AAA_lid_RFC1	e7nprB31	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
B [auth B2]	AAA_lid_RFC1	e7nprB21	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
A [auth B1]	AAA_lid_RFC1	e7nprB11	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth P3], Y [auth P1], Z [auth P2]	PF00082	Subtilase family (Peptidase_S8)	Subtilase family	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7 ...	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.	Domain
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	PF19053	EccD-like transmembrane domain (EccD)	EccD-like transmembrane domain	-	Family
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	PF08817	WXG100 protein secretion system (Wss), protein YukD (YukD)	WXG100 protein secretion system (Wss), protein YukD	The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staph ...	The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold [1]. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins [1]. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway [6,7]. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release [7]. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway [7].	Domain
A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6]	PF05108	Type VII secretion system ESX-1, transport TM domain B (T7SS_ESX1_EccB)	Type VII secretion system ESX-1, transport TM domain B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth P3], Y [auth P1], Z [auth P2]	Mycosin-5	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	ESX-5 secretion system protein EccD5	-	-	cell periphery cellular anatomical structure plasma membrane membrane
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	ESX-5 secretion system protein EccC5	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding	-	cell periphery cellular anatomical structure plasma membrane membrane
A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6]	ESX-5 secretion system ATPase EccB5	-	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth P3], Y [auth P1], Z [auth P2]	IPR015500	Peptidase S8, subtilisin-related	Family
AA [auth P3], Y [auth P1], Z [auth P2]	IPR036852	Peptidase S8/S53 domain superfamily	Homologous Superfamily
AA [auth P3], Y [auth P1], Z [auth P2]	IPR023834	Type VII secretion system peptidase S8A, mycosin	Family
AA [auth P3], Y [auth P1], Z [auth P2]	IPR023827	Peptidase S8, subtilisin, Asp-active site	Active Site
AA [auth P3], Y [auth P1], Z [auth P2]	IPR000209	Peptidase S8/S53 domain	Domain
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	IPR024962	YukD-like	Domain
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	IPR044049	EccD-like transmembrane domain	Domain
M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC]	IPR006707	Type VII secretion system membrane protein EccD	Family
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR002543	FtsK domain	Domain
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR003593	AAA+ ATPase domain	Domain
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR050206	FtsK/SpoIIIE/SftA cell division and DNA translocation	Family
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR023837	EccCb-like, Actinobacteria	Family
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR023836	EccCa-like, Actinobacteria	Family
G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6]	IPR044857	Type VII secretion system EccB, repeat 1 domain	Homologous Superfamily
A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6]	IPR007795	Type VII secretion system EccB	Family
A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], A [auth B1], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6]	IPR042485	Type VII secretion system EccB, repeat 3 domain	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B1], AA [auth P3], B [auth B2], C [auth B3], D [auth B4] A [auth B1], AA [auth P3], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC], Y [auth P1], Z [auth P2]	OPM	Transmembrane	Alpha-helical polytopic	AAA-ATPase superfamily, transmembrane	Type VII (ESX) protein secretion system

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B1], AA [auth P3], B [auth B2], C [auth B3], D [auth B4] A [auth B1], AA [auth P3], B [auth B2], C [auth B3], D [auth B4], E [auth B5], F [auth B6], G [auth C1], H [auth C2], I [auth C3], J [auth C4], K [auth C5], L [auth C6], M [auth D1], N [auth D2], O [auth D3], P [auth D4], Q [auth D5], R [auth D6], S [auth D7], T [auth D8], U [auth D9], V [auth DA], W [auth DB], X [auth DC], Y [auth P1], Z [auth P2]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Type VII Secretion Systems	Mycobacterial secretion system ESX-5 inner membrane complex, Composite C1 model

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.