3PNW | pdb_00003pnw

Crystal Structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 FAB

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8085135	3000404	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)
C	Ribosomal_S8	e3pnwC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_S8	ECOD (v294.1)
F	FAD_binding_4	e3pnwF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
L	FAD_binding_4	e3pnwL1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
R	FAD_binding_4	e3pnwR1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
U	FAD_binding_4	e3pnwU1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
X	FAD_binding_4	e3pnwX1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
O	FAD_binding_4	e3pnwO1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
I	FAD_binding_4	e3pnwI1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
B	Ribosomal_S8	e3pnwB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_S8	ECOD (v294.1)
E	FAD_binding_4	e3pnwE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
H	FAD_binding_4	e3pnwH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
K	FAD_binding_4	e3pnwK1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
N	FAD_binding_4	e3pnwN1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
Q	FAD_binding_4	e3pnwQ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
T	FAD_binding_4	e3pnwT1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
W	FAD_binding_4	e3pnwW1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
A	FAD_binding_4	e3pnwA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
D	FAD_binding_4	e3pnwD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
G	FAD_binding_4	e3pnwG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
J	FAD_binding_4	e3pnwJ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
M	FAD_binding_4	e3pnwM1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
P	FAD_binding_4	e3pnwP1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
S	FAD_binding_4	e3pnwS1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
V	FAD_binding_4	e3pnwV1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
R	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
U	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
X	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
O	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	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)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
N	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
Q	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
T	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
W	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)
D	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)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
P	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
S	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V	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, E, H, K, N B, E, H, K, N, Q, T, W	FAB-GAMMA-1_KAPPA	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202614-0)
A, D, G, J, M A, D, G, J, M, P, S, V	FAB-GAMMA-1_KAPPA	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 (202614-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E, H, K, N B, E, H, K, N, Q, T, W	Heavy Chain	IGHV3	-	tudor domain-containing protein 3	SAbDab (2026-04-17)
A, D, G, J, M A, D, G, J, M, P, S, V	Light Chain	IGKV1	Kappa	tudor domain-containing protein 3	SAbDab (2026-04-17)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L, O C, F, I, L, O, R, U, X	Tudor domain-containing protein 3	histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity RNA binding nucleic acid binding histone H3 reader activity	chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process	protein-containing complex DNA topoisomerase III-beta-TDRD3 complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol nucleus membrane-enclosed lumen protein-containing complex DNA topoisomerase III-beta-TDRD3 complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, E, H, K, N B, E, H, K, N, Q, T, W	FAB heavy chain	-	-	-
A, D, G, J, M A, D, G, J, M, P, S, V	FAB light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L, O C, F, I, L, O, R, U, X	IPR002999	Tudor domain	Domain
C, F, I, L, O C, F, I, L, O, R, U, X	IPR047379	Tudor domain-containing protein 3, Tudor domain	Domain
C, F, I, L, O C, F, I, L, O, R, U, X	IPR013894	RecQ mediated genome instability protein 1, OB-fold domain	Domain
C, F, I, L, O C, F, I, L, O, R, U, X	IPR042470	RecQ mediated genome instability protein, N-terminal OB-fold domain superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R, U, X	IPR041915	Tudor domain-containing protein 3, UBA domain	Domain
C, F, I, L, O C, F, I, L, O, R, U, X	IPR009060	UBA-like superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R, U, X	IPR015940	Ubiquitin-associated domain	Domain