Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9HUJ

CryoEM structure of human peptidylarginine deiminase type 4 (PAD4) in complex with heparin oligomer (12 subunits)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002376	biological_process	immune system process
A	0004668	molecular_function	protein-arginine deiminase activity
A	0005509	molecular_function	calcium ion binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006325	biological_process	chromatin organization
A	0006334	biological_process	nucleosome assembly
A	0006338	biological_process	chromatin remodeling
A	0006351	biological_process	DNA-templated transcription
A	0016787	molecular_function	hydrolase activity
A	0019827	biological_process	stem cell population maintenance
A	0031452	biological_process	negative regulation of heterochromatin formation
A	0032991	cellular_component	protein-containing complex
A	0036211	biological_process	protein modification process
A	0042802	molecular_function	identical protein binding
A	0043687	biological_process	post-translational protein modification
A	0045087	biological_process	innate immune response
A	0046872	molecular_function	metal ion binding
A	0051081	biological_process	nuclear membrane disassembly
A	0140645	biological_process	neutrophil extracellular trap formation
A	0140794	molecular_function	histone arginine deiminase activity
A	0140795	molecular_function	histone H3R2 arginine deiminase activity
A	0140796	molecular_function	histone H3R8 arginine deiminase activity
A	0140797	molecular_function	histone H3R17 arginine deiminase activity
A	0140798	molecular_function	histone H3R26 arginine deiminase activity
B	0002376	biological_process	immune system process
B	0004668	molecular_function	protein-arginine deiminase activity
B	0005509	molecular_function	calcium ion binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0006338	biological_process	chromatin remodeling
B	0006351	biological_process	DNA-templated transcription
B	0016787	molecular_function	hydrolase activity
B	0019827	biological_process	stem cell population maintenance
B	0031452	biological_process	negative regulation of heterochromatin formation
B	0032991	cellular_component	protein-containing complex
B	0036211	biological_process	protein modification process
B	0042802	molecular_function	identical protein binding
B	0043687	biological_process	post-translational protein modification
B	0045087	biological_process	innate immune response
B	0046872	molecular_function	metal ion binding
B	0051081	biological_process	nuclear membrane disassembly
B	0140645	biological_process	neutrophil extracellular trap formation
B	0140794	molecular_function	histone arginine deiminase activity
B	0140795	molecular_function	histone H3R2 arginine deiminase activity
B	0140796	molecular_function	histone H3R8 arginine deiminase activity
B	0140797	molecular_function	histone H3R17 arginine deiminase activity
B	0140798	molecular_function	histone H3R26 arginine deiminase activity
C	0002376	biological_process	immune system process
C	0004668	molecular_function	protein-arginine deiminase activity
C	0005509	molecular_function	calcium ion binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006325	biological_process	chromatin organization
C	0006334	biological_process	nucleosome assembly
C	0006338	biological_process	chromatin remodeling
C	0006351	biological_process	DNA-templated transcription
C	0016787	molecular_function	hydrolase activity
C	0019827	biological_process	stem cell population maintenance
C	0031452	biological_process	negative regulation of heterochromatin formation
C	0032991	cellular_component	protein-containing complex
C	0036211	biological_process	protein modification process
C	0042802	molecular_function	identical protein binding
C	0043687	biological_process	post-translational protein modification
C	0045087	biological_process	innate immune response
C	0046872	molecular_function	metal ion binding
C	0051081	biological_process	nuclear membrane disassembly
C	0140645	biological_process	neutrophil extracellular trap formation
C	0140794	molecular_function	histone arginine deiminase activity
C	0140795	molecular_function	histone H3R2 arginine deiminase activity
C	0140796	molecular_function	histone H3R8 arginine deiminase activity
C	0140797	molecular_function	histone H3R17 arginine deiminase activity
C	0140798	molecular_function	histone H3R26 arginine deiminase activity
D	0002376	biological_process	immune system process
D	0004668	molecular_function	protein-arginine deiminase activity
D	0005509	molecular_function	calcium ion binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0006338	biological_process	chromatin remodeling
D	0006351	biological_process	DNA-templated transcription
D	0016787	molecular_function	hydrolase activity
D	0019827	biological_process	stem cell population maintenance
D	0031452	biological_process	negative regulation of heterochromatin formation
D	0032991	cellular_component	protein-containing complex
D	0036211	biological_process	protein modification process
D	0042802	molecular_function	identical protein binding
D	0043687	biological_process	post-translational protein modification
D	0045087	biological_process	innate immune response
D	0046872	molecular_function	metal ion binding
D	0051081	biological_process	nuclear membrane disassembly
D	0140645	biological_process	neutrophil extracellular trap formation
D	0140794	molecular_function	histone arginine deiminase activity
D	0140795	molecular_function	histone H3R2 arginine deiminase activity
D	0140796	molecular_function	histone H3R8 arginine deiminase activity
D	0140797	molecular_function	histone H3R17 arginine deiminase activity
D	0140798	molecular_function	histone H3R26 arginine deiminase activity

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	15
Details	Active site: {"evidences":[{"source":"PubMed","id":"15247907","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	54
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15247907","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17002273","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	10
Details	Modified residue: {"description":"Citrulline","evidences":[{"source":"PubMed","id":"20201080","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 594

Chain	Residue	Details
A	ASP350	electrostatic stabiliser
A	HIS471	proton acceptor, proton donor
A	ASP473	electrostatic stabiliser
A	CYS645	nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA2
Number of Residues	3
Details	M-CSA 594

Chain	Residue	Details
B	ASP350	electrostatic stabiliser
B	HIS471	proton acceptor, proton donor
B	ASP473	electrostatic stabiliser

site_id	MCSA3
Number of Residues	4
Details	M-CSA 594

Chain	Residue	Details
C	ASP350	electrostatic stabiliser
C	HIS471	proton acceptor, proton donor
C	ASP473	electrostatic stabiliser
C	CYS645	nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA4
Number of Residues	4
Details	M-CSA 594

Chain	Residue	Details
D	ASP350	electrostatic stabiliser
D	HIS471	proton acceptor, proton donor
D	ASP473	electrostatic stabiliser
D	CYS645	nucleofuge, nucleophile, proton acceptor, proton donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)