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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "PADI5"

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

Homo sapiens (18)

Taxonomy

Eukaryota (18)

Experimental Method

	X-RAY DIFFRACTION (16)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (18)

Refinement Resolution (Å)

	2.0 - 2.5 (7)
	2.5 - 3.0 (7)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (5)
	2015 - 2019 (6)
	2020 - 2024 (3)

Enzyme Classification Name

Hydrolases (18)

Symmetry Type

Cyclic (18)

SCOP Classification

	All beta proteins (14)
	Alpha and beta proteins (a+b) (14)

AllSelected

1 to 18 of 18 Structures

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2DEW \| pdb_00002dew	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H3 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2DEX \| pdb_00002dex	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H3 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2DEY \| pdb_00002dey	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H4 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2DW5 \| pdb_00002dw5	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide

Luo, Y., Arita, K., Sato, M., Thompson, P.R.

(2006) Biochemistry 45: 11727-11736

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	BFB, CA, SO4

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3APM \| pdb_00003apm	Download File View File

Crystal structure of the human SNP PAD4 protein

Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 112-118

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)

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3APN \| pdb_00003apn	Download File View File

Crystal structure of the human wild-type PAD4 protein

Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 112-118

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)

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3B1T \| pdb_00003b1t	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-amidine

Causey, C.P., Jones, J.E., Slack, J.L., Kamei, D., Jones Jr, L.E., Subramanian, V., Knuckley, B., Ebrahimi, P., Chumanevich, A.A., Luo, Y., Hashimoto, H., Shimizu, T., Sato, M., Hofseth, L.J., Thompson, P.R.

(2011) J Med Chem 54: 6919-6935

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	CA, SO4, YCL

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3B1U \| pdb_00003b1u	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine

(2011) J Med Chem 54: 6919-6935

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	CA, SO4, YFF

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4DKT \| pdb_00004dkt	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

Jones, J.E., Slack, J.L., Fang, P., Zhang, X., Subramanian, V., Causey, C.P., Coonrod, S.A., Guo, M., Thompson, P.R.

(2012) ACS Chem Biol 7: 160-165

Released	2012-02-29
Method	X-RAY DIFFRACTION 2.98 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein) Thr-Asp-F-amidine (protein)
Unique Ligands	CA, EDO, SO4

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4X8C \| pdb_00004x8c	Download File View File

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK147

Lewis, H.D., Bax, B.D., Chung, C.-W., Polyakova, O., Thorpe, J.

(2015) Nat Chem Biol 11: 189-191

Released	2015-01-28
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	3YZ, CA

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4X8G \| pdb_00004x8g	Download File View File

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199

Lewis, H.D., Bax, B.D., Chung, C.-W., Polyakova, O., Thorpe, J.

(2015) Nat Chem Biol 11: 189-191

Released	2015-01-28
Method	X-RAY DIFFRACTION 3.29 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	3Z0, CA

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5N0M \| pdb_00005n0m	Download File View File

hPAD4 crystal complex with BB-F-amidine

Beaumont, E., Kerry, P., Thompson, P., Muth, A., Subramanian, V., Nagar, M., Srinath, H., Clancy, K., Parelkar, S.

(2017) J Med Chem 60: 3198-3211

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	8HT, CA, SO4

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5N0Y \| pdb_00005n0y	Download File View File

hPAD4 crystal complex with AFM-30a

Beaumont, E., Kerry, P., Thompson, P., Muth, A., Subramanian, V., Nagar, M., Srinath, H., Clancy, K., Parelkar, S.

(2017) J Med Chem 60: 3198-3211

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	8FQ, CA, SO4

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5N0Z \| pdb_00005n0z	Download File View File

hPAD4 crystal complex with AFM-41a

Beaumont, E., Kerry, P., Thompson, P., Muth, A., Subramanian, V., Nagar, M., Srinath, H., Clancy, K., Parelkar, S.

(2017) J Med Chem 60: 3198-3211

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.52 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	8FT, CA, SO4

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5N1B \| pdb_00005n1b	Download File View File

hPAD4 crystal complex with AFM-14a

Beaumont, E., Kerry, P., Thompson, P., Muth, A., Subramanian, V., Nagar, M., Srinath, H., Clancy, K., Parelkar, S.

(2017) J Med Chem 60: 3198-3211

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	8FW, CA, SO4

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8GOD \| pdb_00008god	Download File View File

Co-crystal structure of Human Protein-arginine deiminase type-4 (PAD4) with small molecule inhibitor JBI-589

Swaminathan, S., Birudukota, S., Vaithilingam, K., Kandan, S., Asaithambi, K., Kathiresan, N., Gosu, R., Rajagopal, S., Sadhu, N.

(2023) Sci Rep 13: 3189-3189

Released	2023-03-29
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)
Unique Ligands	K3X

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8SMK \| pdb_00008smk	Download File View File

hPAD4 bound to Activating Fab hA362

Maker, A., Verba, K.A.

(2024) Nat Chem Biol 20: 742-750

Released	2024-03-06
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Activating Fab 362 heavy chain (protein) Activating Fab 362 light chain (protein) Protein-arginine deiminase type-4 (protein)
Unique Ligands	CA

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8SML \| pdb_00008sml	Download File View File

hPAD4 bound to inhibitory Fab hI365

Maker, A., Verba, K.A.

(2024) Nat Chem Biol 20: 742-750

Released	2024-03-06
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Fab hI365 heavy chain (protein) Fab hI365 light chain (protein) Protein-arginine deiminase type-4 (protein)
Unique Ligands	CA

1 to 18 of 18 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.

2DEW | pdb_00002dew

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8

2DEX | pdb_00002dex

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17

2DEY | pdb_00002dey

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3

2DW5 | pdb_00002dw5

Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide

3APM | pdb_00003apm

Crystal structure of the human SNP PAD4 protein

3APN | pdb_00003apn

Crystal structure of the human wild-type PAD4 protein

3B1T | pdb_00003b1t

Crystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-amidine

3B1U | pdb_00003b1u

Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine

4DKT | pdb_00004dkt

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

4X8C | pdb_00004x8c

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK147

4X8G | pdb_00004x8g

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199

5N0M | pdb_00005n0m

hPAD4 crystal complex with BB-F-amidine

5N0Y | pdb_00005n0y

hPAD4 crystal complex with AFM-30a

5N0Z | pdb_00005n0z

hPAD4 crystal complex with AFM-41a

5N1B | pdb_00005n1b

hPAD4 crystal complex with AFM-14a

8GOD | pdb_00008god

Co-crystal structure of Human Protein-arginine deiminase type-4 (PAD4) with small molecule inhibitor JBI-589

8SMK | pdb_00008smk

hPAD4 bound to Activating Fab hA362

8SML | pdb_00008sml

hPAD4 bound to inhibitory Fab hI365

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

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Refinement Resolution (Å)

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Enzyme Classification Name

Symmetry Type

SCOP Classification

2DEW | pdb_00002dew

2DEX | pdb_00002dex

2DEY | pdb_00002dey

2DW5 | pdb_00002dw5

3APM | pdb_00003apm

3APN | pdb_00003apn

3B1T | pdb_00003b1t

3B1U | pdb_00003b1u

4DKT | pdb_00004dkt

4X8C | pdb_00004x8c

4X8G | pdb_00004x8g

5N0M | pdb_00005n0m

5N0Y | pdb_00005n0y

5N0Z | pdb_00005n0z

5N1B | pdb_00005n1b

8GOD | pdb_00008god

8SMK | pdb_00008smk

8SML | pdb_00008sml