6SML

Structure of the RagAB peptide importer in the 'open-open' state

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ASusD_RagBe6smlA1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: SusD_RagBECOD (1.6)
BUNK_F_TYPEe6smlB1 A: beta barrelsX: Outer membrane meander beta-barrelsH: PorinsT: Ligand-gated protein channelF: UNK_F_TYPEECOD (1.6)
BPluge6smlB2 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: TonB-dependent receptor plug domain (From Topology)T: TonB-dependent receptor plug domainF: PlugECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF07980SusD family (SusD_RagB)SusD family- Repeat
PF14322Starch-binding associating with outer membrane (SusD-like_3)Starch-binding associating with outer membrane- Repeat
PF00593TonB dependent receptor-like, beta-barrel (TonB_dep_Rec_b-barrel)TonB dependent receptor-like, beta-barrelThis entry represents the beta-barrel domain of TonB-dependent receptors, such as BtuB, CirA, FatA, FcuT, FecA, FepA, among others [1].Domain
PF07715TonB-dependent Receptor Plug Domain (Plug)TonB-dependent Receptor Plug DomainThe Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens ...The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Lipoprotein RagB- -
RagA protein- -
GLY-THR-GLY-GLY-SER-THR-GLY-THR-THR-SER-ALA-GLY---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR012944RagB/SusD domainDomain
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
IPR033985SusD-like, N-terminalDomain
IPR039426TonB-dependent receptor-likeFamily
IPR037066TonB-dependent receptor, plug domain superfamilyHomologous Superfamily
IPR023997TonB-dependent outer membrane protein SusC/RagA, conserved siteConserved Site
IPR036942TonB-dependent receptor-like, beta-barrel domain superfamilyHomologous Superfamily
IPR023996TonB-dependent outer membrane protein, SusC/RagAFamily
IPR000531TonB-dependent receptor-like, beta-barrelDomain
IPR012910TonB-dependent receptor, plug domainDomain
IPR008969Carboxypeptidase-like, regulatory domain superfamilyHomologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

ChainsExternal LinkTypeClassSuperfamilyFamily
A, B
OPMTransmembraneBeta-barrel transmembraneLigand-gated protein channels (n=22,S=24)Outer Membrane Receptor (OMR)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

ChainsExternal LinkComment
A, B
PDBTMAnnotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

ChainsExternal LinkComment
A, B
MemProtMDAnnotated as membrane protein by MemProtMD