5OCX | pdb_00005ocx

Crystal structure of ACPA E4 in complex with CII-C-13-CIT

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	C1-set_4	e5ocxL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set_3	e5ocxL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B [auth H]	V-set_8	e5ocxH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e5ocxH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGLV1	Lambda	cii-c-13-cit	SAbDab (2025-10-10)
B [auth H]	Heavy Chain	IGHV4	-	cii-c-13-cit	SAbDab (2025-10-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	Fab fragment anti-citrullinated protein antibody E4 - light chain	-	-	-
B [auth H]	Fab fragment of anti-citrullinated protein antibody E4 - heavy chain	-	-	-
C [auth A]	CII-C-13-CIT	protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding carbohydrate derivative binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development carbohydrate derivative metabolic process metabolic process cellular process primary metabolic process developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development carbohydrate derivative metabolic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process limb development appendage development limb bud formation anatomical structure morphogenesis appendage morphogenesis anatomical structure formation involved in morphogenesis limb morphogenesis cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cellular process response to stimulus signal transduction in absence of ligand negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway central nervous system development nervous system development epithelium development otic vesicle development ear development sensory organ development tube development inner ear development embryonic skeletal joint development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development embryonic skeletal joint morphogenesis embryo development ending in birth or egg hatching embryonic skeletal system development animal organ morphogenesis skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis ear morphogenesis sensory organ morphogenesis inner ear morphogenesis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process endochondral ossification replacement ossification endochondral bone morphogenesis ossification bone morphogenesis bone development cell aggregation cartilage condensation cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization heart development heart morphogenesis circulatory system development notochord development system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus sensory perception of light stimulus visual perception multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis cartilage development involved in endochondral bone morphogenesis cellular developmental process cell differentiation chondrocyte differentiation roof of mouth development anterior head development head development cellular response to BMP stimulus cellular response to endogenous stimulus response to BMP cellular response to growth factor stimulus response to endogenous stimulus response to growth factor	basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure protein-containing complex collagen trimer fibrillar collagen trimer complex of collagen trimers fibrillar collagen collagen type XI trimer supramolecular complex collagen type II trimer membrane-bounded organelle basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure protein-containing complex collagen trimer fibrillar collagen trimer complex of collagen trimers fibrillar collagen collagen type XI trimer supramolecular complex collagen type II trimer membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR008160	Collagen triple helix repeat	Repeat
C [auth A]	IPR000885	Fibrillar collagen, C-terminal	Domain
C [auth A]	IPR001007	VWFC domain	Domain
C [auth A]	IPR050149	Collagen superfamily	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: P02458	Kniest dysplasia spondyloepiphyseal dysplasia congenita platyspondylic dysplasia, Torrance type Legg-Calve-Perthes disease mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis spondyloepimetaphyseal dysplasia, Strudwick type spondyloperipheral dysplasia-short ulna syndrome osteochondrodysplasia chondrosarcoma Czech dysplasia, metatarsal type Stickler syndrome, type I, nonsyndromic ocular synovitis cleft palate multiple epiphyseal dysplasia, Beighton type Stickler syndrome type 1 Kniest dysplasia spondyloepiphyseal dysplasia congenita platyspondylic dysplasia, Torrance type Legg-Calve-Perthes disease mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis spondyloepimetaphyseal dysplasia, Strudwick type spondyloperipheral dysplasia-short ulna syndrome osteochondrodysplasia chondrosarcoma Czech dysplasia, metatarsal type Stickler syndrome, type I, nonsyndromic ocular synovitis cleft palate multiple epiphyseal dysplasia, Beighton type Stickler syndrome type 1 melanoma spondyloepiphyseal dysplasia, Stanescu type osteoarthritis Arthritis, Experimental Stickler syndrome achondrogenesis type II cataract achondrogenesis hypochondrogenesis retinal detachment chondromalacia myopia otospondylomegaepiphyseal dysplasia arthritic joint disease Wagner disease cartilage disease spondyloepiphyseal dysplasia multiple epiphyseal dysplasia dysspondyloenchondromatosis hyperplasia avascular necrosis of femoral head, primary, 1 rheumatoid arthritis megaepiphyseal dwarfism Osgood-Schlatter disease osteogenesis imperfecta otospondylomegaepiphyseal dysplasia, autosomal recessive gastric carcinoma pituitary cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor avascular necrosis of femoral head, primary, 2 Schwartz-Jampel syndrome bone resorption disease malignant glioma spondyloepiphyseal dysplasia tarda, X-linked mucopolysaccharidosis type 4 cutaneous melanoma spondylometaphyseal dysplasia, Kozlowski type Ehlers-Danlos syndrome familial avascular necrosis of femoral head glioblastoma prostate carcinoma autosomal dominant rhegmatogenous retinal detachment X-linked mixed deafness with perilymphatic gusher large cell medulloblastoma lung cancer medulloblastoma Melnick-Needles syndrome spondyloepiphyseal dysplasia with congenital joint dislocations spondylometaphyseal dysplasia, 'corner fracture' type spondylometaphyseal dysplasia, Schmidt type osteoarthritis susceptibility 1 osteochondrosis otospondylomegaepiphyseal dysplasia, autosomal dominant pilocytic astrocytoma intellectual disability malignant ependymoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth L]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420
C [auth A]	CIR	Parent Component: ARG RESID: AA0031 , AA0214 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , L-citrulline MOD:00219

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.