3NDZ | pdb_00003ndz

The structure of the catalytic and carbohydrate binding domain of endoglucanase D from Clostridium cellulovorans bound to cellotriose

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d3ndzh_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Carbohydrate-binding domain	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
F [auth G]	d3ndzg_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Carbohydrate-binding domain	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
D [auth F]	d3ndzf_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Carbohydrate-binding domain	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
B [auth E]	d3ndze_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Carbohydrate-binding domain	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
G [auth D]	d3ndzd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
E [auth C]	d3ndzc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
C [auth B]	d3ndzb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)
A	d3ndza_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium cellulovorans ) [TaxId: 1493 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Carbohydrate-binding domain	8073523	3000706	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Carbohydrate-binding domain	8073523	3000706	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Carbohydrate-binding domain	8073523	3000706	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	Carbohydrate-binding domain	8073523	3000706	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	(Trans)glycosidases	8078105	3000313	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	(Trans)glycosidases	8078105	3000313	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	(Trans)glycosidases	8078105	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8078105	3000313	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)
H		e3ndzH1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
F [auth G]		e3ndzG1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
D [auth F]		e3ndzF1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
B [auth E]		e3ndzE1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
G [auth D]		e3ndzD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
E [auth C]		e3ndzC1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
C [auth B]		e3ndzB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)
A		e3ndzA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Carb_anhydrase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.40.290	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
F [auth G]	2.60.40.290	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D [auth F]	2.60.40.290	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B [auth E]	2.60.40.290	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
G [auth D]	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
E [auth C]	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C [auth B]	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], D [auth F], F [auth G], H	PF00553	Cellulose binding domain (CBM_2)	Cellulose binding domain	Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.	Domain
A, C [auth B], E [auth C], G [auth D]	PF00150	Cellulase (glycosyl hydrolase family 5) (Cellulase)	Cellulase (glycosyl hydrolase family 5)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth F], F [auth G], H	Endoglucanase D	hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-glucosidase activity catalytic activity cellulase activity binding polysaccharide binding carbohydrate binding	carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process macromolecule metabolic process cellulose metabolic process	cellular anatomical structure extracellular region cell surface
A, C [auth B], E [auth C], G [auth D]	Endoglucanase D	hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-glucosidase activity catalytic activity cellulase activity binding polysaccharide binding carbohydrate binding	carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process macromolecule metabolic process cellulose metabolic process	cellular anatomical structure extracellular region cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E], D [auth F], F [auth G], H	IPR012291	CBM2, carbohydrate-binding domain superfamily	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR001547	Glycoside hydrolase, family 5	Domain
B [auth E], D [auth F], F [auth G], H	IPR008965	CBM2/CBM3, carbohydrate-binding domain superfamily	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR050386	Glycosyl Hydrolase 5 (Cellulase A)	Family
B [auth E], D [auth F], F [auth G], H	IPR018087	Glycoside hydrolase, family 5, conserved site	Conserved Site
B [auth E], D [auth F], F [auth G], H	IPR001919	Carbohydrate-binding type-2 domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR012291	CBM2, carbohydrate-binding domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR001547	Glycoside hydrolase, family 5	Domain
A, C [auth B], E [auth C], G [auth D]	IPR008965	CBM2/CBM3, carbohydrate-binding domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR050386	Glycosyl Hydrolase 5 (Cellulase A)	Family
A, C [auth B], E [auth C], G [auth D]	IPR018087	Glycoside hydrolase, family 5, conserved site	Conserved Site
A, C [auth B], E [auth C], G [auth D]	IPR001919	Carbohydrate-binding type-2 domain	Domain

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.