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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Oligosaccharide Component List = NAG

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (17)
	Macaca fascicularis (3)
	Rattus norvegicus (3)
	synthetic construct (1)

Taxonomy

	Eukaryota (20)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (7)
	2.0 - 2.5 (8)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (3)
	2015 - 2019 (5)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (6)
	Transferases (2)

Symmetry Type

	Asymmetric (9)
	Cyclic (11)

SCOP Classification

	All beta proteins (6)
	Alpha and beta proteins (a+b) (7)
	All alpha proteins (4)

AllSelected

1 to 20 of 20 Structures

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2JJ3 \| pdb_00002jj3	Download File View File

Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist

Norman, B.H., Richardson, T.I., Dodge, J.A., Pfeifer, L.A., Durst, G.L., Wang, Y., Durbin, J.D., Krishnan, V., Dinn, S.R., Liu, S., Reilly, J.E., Ryter, K.T.

(2007) Bioorg Med Chem Lett 17: 5082

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Homo sapiens
Macromolecule	ESTROGEN RECEPTOR BETA (protein)
Unique Ligands	JJ3

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2POG \| pdb_00002pog	Download File View File

Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure Activity Relationship Studies on the Benzopyran Scaffold.

Richardson, T.I., Norman, B.H., Lugar, C.W., Jones, S.A., Wang, Y., Durbin, J.D., Krishnan, V., Dodge, J.A.

(2007) Bioorg Med Chem Lett 17: 3570-3574

Released	2007-09-11
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Homo sapiens
Macromolecule	Estrogen receptor (protein)
Unique Ligands	WST

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2QE4 \| pdb_00002qe4	Download File View File

Estrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist

Norman, B.H., Richardson, T.I., Dodge, J.A., Pfeifer, L.A., Durst, G.L., Wang, Y., Durbin, J.D., Krishnan, V., Dinn, S.R., Liu, S.Q., Reilly, J.E., Ryter, K.T.

(2007) Bioorg Med Chem Lett 17: 5082-5085

Released	2007-09-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Estrogen receptor (protein)
Unique Ligands	JJ3

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2QTU \| pdb_00002qtu	Download File View File

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand

Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

(2007) Bioorg Med Chem Lett 17: 5563-5566

Released	2007-10-30
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Homo sapiens
Macromolecule	Estrogen receptor beta (protein)
Unique Ligands	3AS

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4WK7 \| pdb_00004wk7	Download File View File

Crystal structure of human ADAMTS-4 in complex with inhibitor (compound 1, 2-(4-chlorophenoxy)-N-{[(4R)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl} acetamide)

Durbin, J.D., Stout, S.L.

(2014) J Med Chem 57: 10476-10485

Released	2014-12-10
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Homo sapiens
Macromolecule	A disintegrin and metalloproteinase with thrombospondin motifs 4 (protein)
Unique Ligands	3PQ, CA, ZN

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4WKE \| pdb_00004wke	Download File View File

Crystal structure of human ADAMTS-4 in complex with inhibitor 5-chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-yl)imidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide (compound 10)

Durbin, J.D.

(2014) J Med Chem 57: 10476-10485

Released	2014-12-10
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Homo sapiens
Macromolecule	A disintegrin and metalloproteinase with thrombospondin motifs 4 (protein)
Unique Ligands	3PU, CA, EDO, ZN

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4WKI \| pdb_00004wki	Download File View File

Crystal structure of human ADAMTS-4 in complex with inhibitor 5-CHLORO-N-{[(4S)-4-(1-METHYL-1H-IMIDAZOL-2-YL)-2,5-DIOXOIMIDAZOLIDIN-4-YL]METHYL}-1-BENZOFURAN-2-CARBOXAMIDE (compound 11)

Durbin, J.D.

(2014) J Med Chem 57: 10476-10485

Released	2014-12-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	A disintegrin and metalloproteinase with thrombospondin motifs 4 (protein)
Unique Ligands	3PW, CA, EDO, ZN

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5L0B \| pdb_00005l0b	Download File View File

Crystal Structure of Autotaxin and Compound 1

Durbin, J.D.

(2016) ACS Med Chem Lett 7: 857-861

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Rattus norvegicus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (protein)
Unique Ligands	6ZM, CL, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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5L0E \| pdb_00005l0e	Download File View File

Crystal Structure of Autotaxin and Compound 1

Durbin, J.D.

(2016) ACS Med Chem Lett 7: 857-861

Released	2016-08-10
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Rattus norvegicus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (protein)
Unique Ligands	6ZN, CL, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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5L0K \| pdb_00005l0k	Download File View File

Crystal Structure of Autotaxin and Compound PF-8380

Durbin, J.D.

(2016) ACS Med Chem Lett 7: 857-861

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.73 Å
Organisms	Rattus norvegicus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (protein)
Unique Ligands	6ZO, CA, CL, EPE, ZN
Unique branched monosaccharides	BMA, NAG

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6NOU \| pdb_00006nou	Download File View File

An scFv derived from ixekizumab

Durbin, J.D., Clawson, D.K., Lu, F., Tian, Y., Lu, J., Atwell, S.

(2019) MAbs 11: 1175-1190

Released	2019-06-19
Method	X-RAY DIFFRACTION 1.914 Å
Organisms	Homo sapiens
Macromolecule	scFv derived from ixekizumab (protein)
Unique Ligands	GOL

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6NOV \| pdb_00006nov	Download File View File

A Fab derived from ixekizumab

Durbin, J.D., Clawson, D.K., Lu, F., Tian, Y., Lu, J., Schmitt, M., Atwell, S.

(2019) MAbs 11: 1175-1190

Released	2019-06-19
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	Homo sapiens
Macromolecule	Fab Heavy Chain (protein) Fab Light Chain (protein)
Unique Ligands	12P

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6UIB \| pdb_00006uib	Download File View File

Crystal structure of IL23 bound to peptide 23-652

Durbin, J.D., Wang, J., Afshar, S.

(2020) PLoS One 15: e0233961-e0233961

Released	2020-07-15
Method	X-RAY DIFFRACTION 2.74 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Interleukin-12 subunit beta (protein) Interleukin-23 subunit alpha (protein) Peptide 23-652 (protein)
Unique branched monosaccharides	NAG

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6WZJ \| pdb_00006wzj	Download File View File

LY3041658 Fab bound to CXCL2

Durbin, J.D., Druzina, Z.

MAbs 12: 1831880-1831880

Released	2020-11-25
Method	X-RAY DIFFRACTION 2.37 Å
Organisms	Homo sapiens Macaca fascicularis
Macromolecule	C-X-C motif chemokine 2 (protein) LY3041658 Fab Heavy Chain (protein) LY3041658 Fab Light Chain (protein)

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6WZK \| pdb_00006wzk	Download File View File

LY3041658 Fab bound to CXCL3

Durbin, J.D., Druzina, Z.

MAbs 12: 1831880-1831880

Released	2020-11-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens Macaca fascicularis
Macromolecule	C-X-C motif chemokine 3 (protein) LY3041658 Fab heavy chain (protein) LY3041658 Fab light chain (protein)
Unique Ligands	ACT, EDO, MG

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6WZL \| pdb_00006wzl	Download File View File

LY3041658 Fab bound to CXCL7

Durbin, J.D., Druzina, Z.

MAbs 12: 1831880-1831880

Released	2020-11-25
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Homo sapiens Macaca fascicularis
Macromolecule	C-X-C motif chemokine 7 (protein) LY3041658 Fab heavy chain (protein) LY3041658 Fab light chain (protein)
Unique Ligands	PG6

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6WZM \| pdb_00006wzm	Download File View File

LY3041658 Fab bound to CXCL8

Durbin, J.D., Druzina, Z.

MAbs 12: 1831880-1831880

Released	2020-11-25
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-8 (protein) LY3041658 Fab heavy chain (protein) LY3041658 Fab light chain (protein)
Unique Ligands	EDO, PG4

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7KCO \| pdb_00007kco	Download File View File

ROR gamma in complex with SCR2 and compound 3

Durbin, J.D., Guo, S.Y., Stout, S.L., Clawson, D.K.

(2021) J Med Chem 64: 5470-5484

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Homo sapiens
Macromolecule	Nuclear receptor ROR-gamma (protein) Peptide GLU-LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER (protein)
Unique Ligands	GOL, WB7

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8UG1 \| pdb_00008ug1	Download File View File

Crystal structure of KHK-C and compound 13

Durbin, J.D., Guo, S.Y.

(2023) J Med Chem 66: 15960-15976

Released	2023-12-06
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	Ketohexokinase (protein)
Unique Ligands	GOL, SO4, WNH

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8UG3 \| pdb_00008ug3	Download File View File

Crystal structure of KHK-C and compound 23

Durbin, J.D., Guo, S.Y.

(2023) J Med Chem 66: 15960-15976

Released	2023-12-06
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Homo sapiens
Macromolecule	Ketohexokinase (protein)
Unique Ligands	GOL, SO4, WRE

1 to 20 of 20 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.

2JJ3 | pdb_00002jj3

Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist

2POG | pdb_00002pog

Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure Activity Relationship Studies on the Benzopyran Scaffold.

2QE4 | pdb_00002qe4

Estrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist

2QTU | pdb_00002qtu

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand

4WK7 | pdb_00004wk7

Crystal structure of human ADAMTS-4 in complex with inhibitor (compound 1, 2-(4-chlorophenoxy)-N-{[(4R)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl} acetamide)

4WKE | pdb_00004wke

Crystal structure of human ADAMTS-4 in complex with inhibitor 5-chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-yl)imidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide (compound 10)

4WKI | pdb_00004wki

Crystal structure of human ADAMTS-4 in complex with inhibitor 5-CHLORO-N-{[(4S)-4-(1-METHYL-1H-IMIDAZOL-2-YL)-2,5-DIOXOIMIDAZOLIDIN-4-YL]METHYL}-1-BENZOFURAN-2-CARBOXAMIDE (compound 11)

5L0B | pdb_00005l0b

Crystal Structure of Autotaxin and Compound 1

5L0E | pdb_00005l0e

Crystal Structure of Autotaxin and Compound 1

5L0K | pdb_00005l0k

Crystal Structure of Autotaxin and Compound PF-8380

6NOU | pdb_00006nou

An scFv derived from ixekizumab

6NOV | pdb_00006nov

A Fab derived from ixekizumab

6UIB | pdb_00006uib

Crystal structure of IL23 bound to peptide 23-652

6WZJ | pdb_00006wzj

LY3041658 Fab bound to CXCL2

6WZK | pdb_00006wzk

LY3041658 Fab bound to CXCL3

6WZL | pdb_00006wzl

LY3041658 Fab bound to CXCL7

6WZM | pdb_00006wzm

LY3041658 Fab bound to CXCL8

7KCO | pdb_00007kco

ROR gamma in complex with SCR2 and compound 3

8UG1 | pdb_00008ug1

Crystal structure of KHK-C and compound 13

8UG3 | pdb_00008ug3

Crystal structure of KHK-C and compound 23

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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

2JJ3 | pdb_00002jj3

2POG | pdb_00002pog

2QE4 | pdb_00002qe4

2QTU | pdb_00002qtu

4WK7 | pdb_00004wk7

4WKE | pdb_00004wke

4WKI | pdb_00004wki

5L0B | pdb_00005l0b

5L0E | pdb_00005l0e

5L0K | pdb_00005l0k

6NOU | pdb_00006nou

6NOV | pdb_00006nov

6UIB | pdb_00006uib

6WZJ | pdb_00006wzj

6WZK | pdb_00006wzk

6WZL | pdb_00006wzl

6WZM | pdb_00006wzm

7KCO | pdb_00007kco

8UG1 | pdb_00008ug1

8UG3 | pdb_00008ug3