5XAM | pdb_00005xam

Crystal structure of SecDF in I form at 4 A resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
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)
A	secD	e5xamA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: secD	ECOD (1.6)
A	SecD_SecF	e5xamA2	A: alpha bundles	X: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	H: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	T: Multidrug efflux transporter AcrB transmembrane domain	F: SecD_SecF	ECOD (1.6)
A	secD_1	e5xamA3	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: secD_1	ECOD (1.6)
A	3a0501s07	e5xamA5	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: 3a0501s07	ECOD (1.6)
B	secD	e5xamB3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: secD	ECOD (1.6)
B	SecD_SecF	e5xamB5	A: alpha bundles	X: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	H: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	T: Multidrug efflux transporter AcrB transmembrane domain	F: SecD_SecF	ECOD (1.6)
B	secD_1	e5xamB4	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: secD_1	ECOD (1.6)
B	3a0501s07	e5xamB1	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: 3a0501s07	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.3220	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.1360.200	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	3.30.70.3220	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21760	Protein translocase subunit SecDF, P1 domain, N-terminal (SecD_1st)	Protein translocase subunit SecDF, P1 domain, N-terminal	This domain is found in Protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the ...	This domain is found in Protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the base subdomain of the P1 domain that is located in the N- terminal half of the polypeptide, also known as SecD region. This domain folds into a a pseudo-symmetrical anti-parallel beta-sheet that rearranges to a beta-barrel architecture during ion transport. This domain, which covers the TM region [1-4], is related to Pfam:PF03176 and usually appears associated with Pfam:PF07549 and Pfam:PF02355.	Domain
A, B	PF22599	SecDF, P1 head subdomain (SecDF_P1_head)	SecDF, P1 head subdomain	This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport [1-3]. P1 domain P1 binds an unfolded protein, and undergoes functionally important conformational changes. SecDF f ...	This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport [1-3]. P1 domain P1 binds an unfolded protein, and undergoes functionally important conformational changes. SecDF functions as a membrane-integrated chaperone that mediates ATP-independent protein translocation.	Domain
A, B	PF02355	Protein export membrane protein SecD/SecF, C-terminal (SecD_SecF_C)	Protein export membrane protein SecD/SecF, C-terminal	This entry represents the C-terminal domain of various prokaryotic SecD and SecF protein export membrane proteins and their archaeal homologues. These SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, ...	This entry represents the C-terminal domain of various prokaryotic SecD and SecF protein export membrane proteins and their archaeal homologues. These SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC[1]. SecD and SecF are required to maintain a proton motive force [2].	Domain
A, B	PF07549	SecD/SecF GG Motif (Sec_GG)	SecD/SecF GG Motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein translocase subunit SecD	macromolecule transmembrane transporter activity active transmembrane transporter activity protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein transmembrane transporter activity protein-transporting ATPase activity transporter activity transmembrane transporter activity ATP-dependent activity	localization establishment of protein localization protein targeting establishment of localization cellular localization nitrogen compound transport transport intracellular protein transmembrane transport intracellular transport transmembrane transport protein transmembrane transport protein transport macromolecule localization establishment of localization in cell localization establishment of protein localization protein targeting establishment of localization cellular localization nitrogen compound transport transport intracellular protein transmembrane transport intracellular transport transmembrane transport protein transmembrane transport protein transport macromolecule localization establishment of localization in cell cellular process intracellular protein localization intracellular protein transport protein transport by the Sec complex	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054384	SecDF, P1 head subdomain	Domain
A, B	IPR005665	Protein-export membrane protein SecF, bacterial	Family
A, B	IPR055344	Protein-export membrane protein SecD/SecF, C-terminal, bacterial	Domain
A, B	IPR022646	Protein-export membrane protein SecD/SecF/SecDF, conserved site	Conserved Site
A, B	IPR000731	Sterol-sensing domain	Domain
A, B	IPR022645	Protein-export membrane protein SecD/SecF, bacterial	Family
A, B	IPR048631	Protein translocase subunit SecDF, P1 domain, N-terminal	Domain
A, B	IPR022813	Protein-export membrane protein SecD/SecF, archaeal and bacterial	Family
A, B	IPR048634	Protein export membrane protein SecD/SecF, C-terminal	Domain
A, B	IPR005791	Protein translocase subunit SecD	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Resistance-nodulation-cell division	SecDF protein-export membrane protein

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	SecDF protein-export enhancer in I form, wild-type

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.