6VMJ | pdb_00006vmj

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L [auth Z]	d6vmjz_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Factor D	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth Y]	d6vmjy_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Factor D	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth X]	d6vmjx_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Factor D	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I [auth W]	d6vmjw_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Factor D	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth M]	d6vmjm_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth J]	d6vmjj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth F]	d6vmjf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6vmjb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth L]	d6vmjl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth L]	d6vmjl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d6vmji2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d6vmji1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d6vmje2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d6vmje1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6vmja2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6vmja1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth Z]	SCOP2B Superfamily	Trypsin-like serine proteases	8042234	3000114	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	Trypsin-like serine proteases	8042234	3000114	SCOP2B (2022-06-29)
J [auth X]	SCOP2B Superfamily	Trypsin-like serine proteases	8042234	3000114	SCOP2B (2022-06-29)
I [auth W]	SCOP2B Superfamily	Trypsin-like serine proteases	8042234	3000114	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth Z]		e6vmjZ1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
K [auth Y]		e6vmjY1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
J [auth X]		e6vmjX1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
I [auth W]		e6vmjW1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
H [auth M]		e6vmjM1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
F [auth J]		e6vmjJ1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
D [auth F]		e6vmjF1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
B		e6vmjB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
G [auth L]		e6vmjL1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
E [auth I]		e6vmjI1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
C [auth E]		e6vmjE1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)
A		e6vmjA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
G [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	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
B, D [auth F], F [auth J], H [auth M]	Heavy Chain	IGHV1	-	complement factor d	SAbDab (2026-03-27)
A, C [auth E], E [auth I], G [auth L]	Light Chain	IGKV1	Kappa	complement factor d	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth W], J [auth X], K [auth Y], L [auth Z]	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth W], J [auth X], K [auth Y], L [auth Z]	Complement factor D	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation humoral immune response positive regulation of biological process complement activation, alternative pathway positive regulation of response to stimulus complement activation positive regulation of immune response response to stress innate immune response regulation of immune system process positive regulation of immune system process regulation of biological process immune response defense response biological regulation defense response to symbiont immune effector process regulation of response to stimulus immune system process defense response to other organism regulation of immune response activation of immune response proteolysis zymogen activation protein processing	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen secretory granule secretory vesicle cytoplasm platelet alpha granule platelet alpha granule lumen ficolin-1-rich granule ficolin-1-rich granule lumen
B, D [auth F], F [auth J], H [auth M]	Fab20D12 heavy chain	-	-	-
A, C [auth E], E [auth I], G [auth L]	Fab20D12 Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR001314	Peptidase S1A, chymotrypsin family	Family
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR001254	Serine proteases, trypsin domain	Domain
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth W], J [auth X], K [auth Y], L [auth Z]	Pharos: P00746	recurrent Neisseria infections due to factor D deficiency glomerulonephritis meningococcal infection endometriosis Neisseriaceae Infections congestive heart failure pulmonary fibrosis asbestosis primary immunodeficiency disease idiopathic interstitial pneumonia limb-girdle muscular dystrophy lung cancer malignant mesothelioma adrenal cortex carcinoma ovarian cyst recurrent Neisseria infections due to factor D deficiency glomerulonephritis meningococcal infection endometriosis Neisseriaceae Infections congestive heart failure pulmonary fibrosis asbestosis primary immunodeficiency disease idiopathic interstitial pneumonia limb-girdle muscular dystrophy lung cancer malignant mesothelioma adrenal cortex carcinoma ovarian cyst atopic eczema pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast carcinoma psoriasis ductal breast carcinoma in situ heart failure invasive ductal breast carcinoma lung carcinoma non-small cell lung carcinoma B-cell chronic lymphocytic leukemia primary biliary cholangitis breast fibroadenoma corpus luteum cyst Sjogren syndrome lung adenocarcinoma malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous carcinoma breast cancer Duchenne muscular dystrophy tuberculosis

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.