9FZC

Structure of OmpA-short in complex with nanobody Nb01

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	OMPA barrel-like	8032699	3000208	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	OMPA barrel-like	8032699	3000208	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	outer membrane protein a	SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01389	OmpA-like transmembrane domain (OmpA_membrane)	OmpA-like transmembrane domain	The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Outer membrane protein A	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity monoatomic ion transmembrane transporter activity identical protein binding protein binding binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction response to other organism detection of virus response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	membrane cellular anatomical entity outer membrane protein-containing complex outer membrane protein complex membrane protein complex outer membrane-bounded periplasmic space cell envelope periplasmic space pore complex cell periphery cell outer membrane external encapsulating structure
C, D	Nanobody 01	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006664	Outer membrane protein, bacterial	Domain
A, B	IPR000498	Outer membrane protein OmpA-like, transmembrane domain	Domain
A, B	IPR006690	Outer membrane protein, OmpA-like, conserved site	Conserved Site
A, B	IPR050330	Bacterial Outer Membrane Structural/Functional	Family
A, B	IPR036737	OmpA-like domain superfamily	Homologous Superfamily
A, B	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B	IPR006665	OmpA-like domain	Domain
A, B	IPR002368	Outer membrane protein, OmpA	Family

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

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.