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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.4.21.69

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This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Homo sapiens (10)
	Escherichia phage EcSzw-2 (2)
	Influenza A virus (A/Victoria/3/1975(H3N2)) (2)
	Bos taurus (1)

Taxonomy

	Eukaryota (10)
	Duplodnaviria (2)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (7)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (10)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (1)
	2.5 - 3.0 (2)
	3.0 - 3.5 (2)
	3.5 - 4.0 (2)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (2)
	2020 - 2024 (4)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (10)
	Lyases (1)

Membrane Protein Annotation

	mpstruc (2)
	OPM (1)

Symmetry Type

Asymmetric (10)

SCOP Classification

	All beta proteins (3)
	Small proteins (4)
	Alpha and beta proteins (a+b) (2)

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1 to 10 of 10 Structures

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1AUT \| pdb_00001aut	Download File View File

Human activated protein C

Mather, T., Oganessyan, V., Hof, P., Bode, W., Huber, R., Foundling, S., Esmon, C.

(1996) EMBO J 15: 6822-6831

Released	1997-08-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	ACTIVATED PROTEIN C (protein)
Unique Ligands	0G6

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1LQV \| pdb_00001lqv	Download File View File

Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C.

Oganesyan, V., Oganesyan, N., Terzyan, S., Dongfeng, Q., Dauter, Z., Esmon, N.L., Esmon, C.T.

(2002) J Biological Chem 277: 24851-24854

Released	2002-06-19
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Endothelial protein C receptor (protein) Vitamin-K dependent protein C (protein)
Unique Ligands	CA, NAG, PTY

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3F6U \| pdb_00003f6u	Download File View File

Crystal structure of human Activated Protein C (APC) complexed with PPACK

Schmidt, A.E., Padmanabhan, K., Underwood, M.C., Bode, W., Mather, T., Bajaj, S.P.

(2002) J Biological Chem 277: 28987-28995

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Vitamin K-dependent protein C heavy chain (protein) Vitamin K-dependent protein C light chain (protein)
Unique Ligands	0G6, CA, NA

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3JTC \| pdb_00003jtc	Download File View File

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins

Bajaj, S.P., Vadivel, K., Agah, S., Cascio, D., Krishnaswamy, S., Esmon, C., Padmanabhan, K.

(2013) J Mol Biology 425: 1961-1981

Released	2011-04-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Endothelial protein C receptor (protein) Vitamin K-dependent protein C (protein)
Unique Ligands	CA, MG, NAG, PTY

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4DT7 \| pdb_00004dt7	Download File View File

Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C

Pozzi, N., Barranco-Medina, S., Chen, Z., Di Cera, E.

(2012) Blood 120: 664-670

Released	2012-05-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) Vitamin K-dependent protein C (protein)
Unique Ligands	ACT, NA, PEG

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6M3B \| pdb_00006m3b	Download File View File

hAPC-c25k23 Fab complex

Wang, X., Li, L., Zhao, X., Egner, U.

(2020) Nat Commun 11: 2992-2992

Released	2020-07-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Vitamin K-dependent protein C heavy chain (protein) Vitamin K-dependent protein C light chain (protein) c25k23 Fab H chain (protein) c25k23 Fab L chain (protein)
Unique Ligands	NAG

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6M3C \| pdb_00006m3c	Download File View File

hAPC-h1573 Fab complex

Wang, X., Wang, D., Zhao, X., Egner, U.

(2020) Nat Commun 11: 2992-2992

Released	2020-07-08
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Homo sapiens
Macromolecule	Vitamin K-dependent protein C heavy chain (protein) Vitamin K-dependent protein C light chain (protein) h1573 Fab H chain (protein) h1573 Fab L chain (protein)

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8JRU \| pdb_00008jru	Download File View File

Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state

Chen, K., Zhang, C., Lin, S., Zhao, Q., Wu, B.

(2023) Nature 620: 904-910

Released	2023-08-16
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Bos taurus Escherichia phage EcSzw-2 Homo sapiens Influenza A virus (A/Victoria/3/1975(H3N2))
Macromolecule	Beta-arrestin 1 and single-chain fragment variable 30 (scFv30) (protein) HA signal peptide,HPC4 purification tag,Glucagon receptor,C-terminal tail of Vasopressin V2 receptor (protein) Nanobody 32 (protein)
Unique Ligands	PIO

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8JRV \| pdb_00008jrv	Download File View File

Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1

Chen, K., Zhang, C., Lin, S., Zhao, Q., Wu, B.

(2023) Nature 620: 904-910

Released	2023-08-16
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Escherichia phage EcSzw-2 Homo sapiens Influenza A virus (A/Victoria/3/1975(H3N2))
Macromolecule	Beta-arrestin 1 and single-chain fragment variable 30 (scFv30) (protein) Glucagon (protein) HA signal peptide,HPC4 purification tag,Glucagon receptor,C-terminal tail of Vasopressin V2 receptor (protein) Nanobody 32 (protein)
Unique Ligands	PIO

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9BVM \| pdb_00009bvm	Download File View File

Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone

Li, W., Liu, B., Cao, Q.

(2025) Nature 639: 816-824

Released	2025-01-22
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Activation peptide (protein) Vitamin K-dependent gamma-carboxylase (protein)
Unique Ligands	6PL, A1AVC, NAG
Unique branched monosaccharides	NAG

1 to 10 of 10 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.

1AUT | pdb_00001aut

Human activated protein C

1LQV | pdb_00001lqv

Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C.

3F6U | pdb_00003f6u

Crystal structure of human Activated Protein C (APC) complexed with PPACK

3JTC | pdb_00003jtc

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins

4DT7 | pdb_00004dt7

Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C

6M3B | pdb_00006m3b

hAPC-c25k23 Fab complex

6M3C | pdb_00006m3c

hAPC-h1573 Fab complex

8JRU | pdb_00008jru

Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state

8JRV | pdb_00008jrv

Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1

9BVM | pdb_00009bvm

Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1AUT | pdb_00001aut

1LQV | pdb_00001lqv

3F6U | pdb_00003f6u

3JTC | pdb_00003jtc

4DT7 | pdb_00004dt7

6M3B | pdb_00006m3b

6M3C | pdb_00006m3c

8JRU | pdb_00008jru

8JRV | pdb_00008jrv

9BVM | pdb_00009bvm