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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "PAD4"

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

	Homo sapiens (7)
	Mus musculus (6)
	Arabidopsis thaliana (2)

Taxonomy

Eukaryota (15)

Experimental Method

	X-RAY DIFFRACTION (12)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (15)

Refinement Resolution (Å)

	2.0 - 2.5 (3)
	2.5 - 3.0 (7)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	2015 - 2019 (10)
	2020 - 2024 (5)

Enzyme Classification Name

	Hydrolases (13)
	Transferases (2)

Symmetry Type

	Asymmetric (8)
	Cyclic (7)

SCOP Classification

	All beta proteins (8)
	Alpha and beta proteins (a+b) (8)
	Artifacts (1)

AllSelected

1 to 15 of 15 Structures

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Explore in 3D

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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6MKD \| pdb_00006mkd	Download File View File

4699 TCR bound to I-Ab Padi4

Stadinski, B.D., Blevins, S.J., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mus musculus
Macromolecule	4699 TCR alpha chain (protein) 4699 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain (protein)

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6MKR \| pdb_00006mkr	Download File View File

5287 TCR bound to IAb Padi4

Stadinski, B.D., Blevins, S.J., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 3.355 Å
Organisms	Mus musculus
Macromolecule	5287 TCR alpha chain (protein) 5287 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi 4 (92-105) peptide and MHC Class II IAb beta chain (protein)

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6MNG \| pdb_00006mng	Download File View File

4738 TCR bound to IAb Padi4

Blevins, S.J., Stadinski, B.D., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.662 Å
Organisms	Mus musculus
Macromolecule	4738 TCR alpha chain (protein) 4738 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi4 (92-105) peptide and MHCII I-Ab beta chain (protein)

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6MNM \| pdb_00006mnm	Download File View File

6256 TCR bound to I-Ab Padi4

Blevins, S.J., Stadinski, B.D., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Mus musculus
Macromolecule	6256 TCR alpha chain (protein) 6256 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi4 (92-105) peptide and MHC Class II I-Ab beta chain (protein)

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6MNN \| pdb_00006mnn	Download File View File

6236 TCR bound to I-Ab Padi4

Blevins, S.J., Stadinski, B.D., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.83 Å
Organisms	Mus musculus
Macromolecule	6236 TCR alpha chain (protein) 6236 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi4 (92-105) peptide and MHC Class II I-Ab beta chain (protein)

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6MNO \| pdb_00006mno	Download File View File

6235 TCR bound to I-Ab Padi4

Stadinski, B.D., Blevins, S.J., Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Mus musculus
Macromolecule	6235 TCR alpha chain (protein) 6235 TCR beta chain (protein) H-2 class II histocompatibility antigen, A-B alpha chain (protein) Padi4 (92-105) peptide and MHC Class II I-Ab beta chain (protein)

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7XDD \| pdb_00007xdd	Download File View File

Cryo-EM structure of EDS1 and PAD4

Huang, S.J., Jia, A.L., Sun, Y., Han, Z.F., Chai, J.J.

(2022) Science 377: eabq3297-eabq3297

Released	2022-07-13
Method	ELECTRON MICROSCOPY 2.93 Å
Organisms	Arabidopsis thaliana
Macromolecule	Lipase-like PAD4 (protein) Protein EDS1 (protein)

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7XEY \| pdb_00007xey	Download File View File

EDS1-PAD4 complexed with pRib-ADP

Huang, S., Jia, A., Xiao, Y.

(2022) Science 377: eabq3297-eabq3297

Released	2022-07-13
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Arabidopsis thaliana
Macromolecule	Lipase-like PAD4 (protein) Protein EDS1 (protein)
Unique Ligands	ADP, RP5, TRS

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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 15 of 15 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.

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

6MKD | pdb_00006mkd

4699 TCR bound to I-Ab Padi4

6MKR | pdb_00006mkr

5287 TCR bound to IAb Padi4

6MNG | pdb_00006mng

4738 TCR bound to IAb Padi4

6MNM | pdb_00006mnm

6256 TCR bound to I-Ab Padi4

6MNN | pdb_00006mnn

6236 TCR bound to I-Ab Padi4

6MNO | pdb_00006mno

6235 TCR bound to I-Ab Padi4

7XDD | pdb_00007xdd

Cryo-EM structure of EDS1 and PAD4

7XEY | pdb_00007xey

EDS1-PAD4 complexed with pRib-ADP

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

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

5N0M | pdb_00005n0m

5N0Y | pdb_00005n0y

5N0Z | pdb_00005n0z

5N1B | pdb_00005n1b

6MKD | pdb_00006mkd

6MKR | pdb_00006mkr

6MNG | pdb_00006mng

6MNM | pdb_00006mnm

6MNN | pdb_00006mnn

6MNO | pdb_00006mno

7XDD | pdb_00007xdd

7XEY | pdb_00007xey

8GOD | pdb_00008god

8SMK | pdb_00008smk

8SML | pdb_00008sml