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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 2.1.1.28

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Homo sapiens (7)
	Bifidobacterium bifidum (4)
	Elizabethkingia meningoseptica (2)
	Gallus gallus (2)
	Halalkalibacterium halodurans C-125 (1)

Taxonomy

	Eukaryota (9)
	Bacteria (7)

Experimental Method

X-RAY DIFFRACTION (16)

Polymer Entity Type

Protein (16)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (5)
	2.0 - 2.5 (8)
	2.5 - 3.0 (2)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (7)
	2010 - 2014 (3)
	2015 - 2019 (4)

Enzyme Classification Name

Hydrolases (16)

Symmetry Type

	Cyclic (12)
	Asymmetric (4)

SCOP Classification

	All beta proteins (9)
	Alpha and beta proteins (a/b) (9)
	Artifacts (3)

AllSelected

1 to 16 of 16 Structures

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1KTB \| pdb_00001ktb	Download File View File

The Structure of alpha-N-Acetylgalactosaminidase

Garman, S.C., Hannick, L., Zhu, A., Garboczi, D.N.

(2002) Structure 10: 425-434

Released	2002-03-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Gallus gallus
Macromolecule	alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	ACY, GOL, NAG, SO4
Unique branched monosaccharides	NAG

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1KTC \| pdb_00001ktc	Download File View File

The Structure of alpha-N-Acetylgalactosaminidase

Garman, S.C., Hannick, L., Zhu, A., Garboczi, D.N.

(2002) Structure 10: 425-434

Released	2002-03-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Gallus gallus
Macromolecule	alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	ACY, GOL, NAG, NGA, SO4
Unique branched monosaccharides	NAG

Explore in 3D

2IXA \| pdb_00002ixa	Download File View File

A-zyme, N-acetylgalactosaminidase

Sulzenbacher, G., Liu, Q.P., Bourne, Y., Henrissat, B., Clausen, H.

(2007) Nat Biotechnol 25: 454

Released	2007-04-10
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Elizabethkingia meningoseptica
Macromolecule	ALPHA-N-ACETYLGALACTOSAMINIDASE (protein)
Unique Ligands	MPD, MRD, NAD

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2IXB \| pdb_00002ixb	Download File View File

Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC

Sulzenbacher, G., Liu, Q.P., Bourne, Y., Henrissat, B., Clausen, H.

(2007) Nat Biotechnol 25: 454

Released	2007-04-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Elizabethkingia meningoseptica
Macromolecule	ALPHA-N-ACETYLGALACTOSAMINIDASE (protein)
Unique Ligands	A2G, MPD, MRD, NAD

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3CC1 \| pdb_00003cc1	Download File View File

CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

Joint Center for Structural Genomics (JCSG)

To be published

Released	2008-03-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Halalkalibacterium halodurans C-125
Macromolecule	Putative alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	GOL, IMD, P33, PEG, PG4, PGE, SO4

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3H53 \| pdb_00003h53	Download File View File

Crystal Structure of human alpha-N-acetylgalactosaminidase

Clark, N.E., Garman, S.C.

(2009) J Mol Biology 393: 435-447

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	GOL, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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3H54 \| pdb_00003h54	Download File View File

Crystal Structure of human alpha-N-acetylgalactosaminidase,complex with GalNAc

Clark, N.E., Garman, S.C.

(2009) J Mol Biology 393: 435-447

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	A2G, GOL, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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3H55 \| pdb_00003h55	Download File View File

Crystal Structure of human alpha-N-acetylgalactosaminidase, Complex with Galactose

Clark, N.E., Garman, S.C.

(2009) J Mol Biology 393: 435-447

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	CIT, GLA, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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3IGU \| pdb_00003igu	Download File View File

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

Clark, N.E., Garman, S.C.

(2009) J Mol Biology 393: 435-447

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	7JZ, GOL, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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4DO4 \| pdb_00004do4	Download File View File

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Clark, N.E., Garman, S.C.

(2012) Proc Natl Acad Sci U S A 109: 17400-17405

Released	2012-10-10
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	ACY, CIT, DJN, GOL, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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4DO5 \| pdb_00004do5	Download File View File

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Clark, N.E., Garman, S.C.

(2012) Proc Natl Acad Sci U S A 109: 17400-17405

Released	2012-10-10
Method	X-RAY DIFFRACTION 1.51 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	CIT, DGJ, GOL, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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4DO6 \| pdb_00004do6	Download File View File

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Clark, N.E., Garman, S.C.

(2012) Proc Natl Acad Sci U S A 109: 17400-17405

Released	2012-10-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	2PE, BGC, CIT, GLC, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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5WZN \| pdb_00005wzn	Download File View File

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc complex

Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.

(2017) J Biological Chem 292: 12126-12138

Released	2017-06-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bifidobacterium bifidum
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	A2G, CA, ZN

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5WZP \| pdb_00005wzp	Download File View File

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free

Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.

(2017) J Biological Chem 292: 12126-12138

Released	2017-06-07
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Bifidobacterium bifidum
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	CA, ZN

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5WZQ \| pdb_00005wzq	Download File View File

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - quadruple mutant

Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.

(2017) J Biological Chem 292: 12126-12138

Released	2017-06-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bifidobacterium bifidum
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	GOL, ZN

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5WZR \| pdb_00005wzr	Download File View File

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex

Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.

(2017) J Biological Chem 292: 12126-12138

Released	2017-06-07
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Bifidobacterium bifidum
Macromolecule	Alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	CA, DJN, ZN

1 to 16 of 16 Structures

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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.

1KTB | pdb_00001ktb

The Structure of alpha-N-Acetylgalactosaminidase

1KTC | pdb_00001ktc

The Structure of alpha-N-Acetylgalactosaminidase

2IXA | pdb_00002ixa

A-zyme, N-acetylgalactosaminidase

2IXB | pdb_00002ixb

Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC

3CC1 | pdb_00003cc1

CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

3H53 | pdb_00003h53

Crystal Structure of human alpha-N-acetylgalactosaminidase

3H54 | pdb_00003h54

Crystal Structure of human alpha-N-acetylgalactosaminidase,complex with GalNAc

3H55 | pdb_00003h55

Crystal Structure of human alpha-N-acetylgalactosaminidase, Complex with Galactose

3IGU | pdb_00003igu

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

4DO4 | pdb_00004do4

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

4DO5 | pdb_00004do5

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

4DO6 | pdb_00004do6

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

5WZN | pdb_00005wzn

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc complex

5WZP | pdb_00005wzp

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free

5WZQ | pdb_00005wzq

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - quadruple mutant

5WZR | pdb_00005wzr

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1KTB | pdb_00001ktb

1KTC | pdb_00001ktc

2IXA | pdb_00002ixa

2IXB | pdb_00002ixb

3CC1 | pdb_00003cc1

3H53 | pdb_00003h53

3H54 | pdb_00003h54

3H55 | pdb_00003h55

3IGU | pdb_00003igu

4DO4 | pdb_00004do4

4DO5 | pdb_00004do5

4DO6 | pdb_00004do6

5WZN | pdb_00005wzn

5WZP | pdb_00005wzp

5WZQ | pdb_00005wzq

5WZR | pdb_00005wzr