5C8J | pdb_00005c8j

A YidC-like protein in the archaeal plasma membrane

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2 Family	EMC3/TMCO1-like	8049788	4006639	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	YidC transmembrane domain-like	8101848	3002720	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	EMC3_TMCO1	e5c8jI1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F: EMC3_TMCO1	ECOD (v294.1)
J	YkuD	e5c8jJ1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
K	YkuD	e5c8jK1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
L	EMC3_TMCO1	e5c8jL1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F: EMC3_TMCO1	ECOD (v294.1)
B	DEAD_2	e5c8jB1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
D	DEAD_2	e5c8jD1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
F	DEAD_2	e5c8jF1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
H	DEAD_2	e5c8jH1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
A	DEAD_2	e5c8jA2	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
A	EF-hand_1, EF-hand_6, EF-hand_7	e5c8jA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
C	DEAD_2	e5c8jC2	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
C	EF-hand_1, EF-hand_6, EF-hand_7	e5c8jC3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
E	DEAD_2	e5c8jE1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
E	EF-hand_1, EF-hand_6, EF-hand_7	e5c8jE2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
G	DEAD_2	e5c8jG2	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: DEAD_2	ECOD (v294.1)
G	EF-hand_1, EF-hand_6, EF-hand_7	e5c8jG3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D, F, H	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)
A, C, E, G	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H	Light Chain	IGKV1	Kappa	protein mj0480	SAbDab (2026-03-27)
A, C, E, G	Heavy Chain	IGHV3	-	protein mj0480	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I, J, K, L	PF01956	Integral membrane protein EMC3/TMCO1-like (EMC3_TMCO1)	Integral membrane protein EMC3/TMCO1-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L	Protein MJ0480	binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
B, D, F, H	Antibody fragment, light chain	-	-	-
A, C, E, G	Antibody fragment, heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR038978	Protein MJ0935	Family
I, J, K, L	IPR002809	Integral membrane protein EMC3/TMCO1-like	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
I, J, K, L	OPM	Transmembrane	Alpha-helical polytopic	Cytochrome oxidase biogenesis family	OxaA/YidC

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
I, J, K, L	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
I, J, K, L	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	DUF106 YidC-like protein

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.

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