1WD9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CALCIUM BOUND FORM OF HUMAN PEPTIDYLARGININE DEIMINASE TYPE4 (PAD4)

Authors :   K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato

Date :   12 May 04 (Deposition) - 13 Jul 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Post-Translational Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato
Structural Basis For Ca(2+)-Induced Activation Of Human Pad
Nat. Struct. Mol. Biol. V. 11 777 2004
PubMed-ID: 15247907 | Reference-DOI: 10.1038/NSMB799

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE IV
	Chains	:	A
	EC Number	:	3.5.3.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PEPTIDYLARGININE DEIMINASE IV, HL-60 PAD

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	5	Ligand/Ion	CALCIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:349 , GLU A:353 , PHE A:407 , LEU A:410 , GLU A:411	BINDING SITE FOR RESIDUE CA A 900
2	AC2	SOFTWARE	ASN A:153 , ASP A:155 , ASP A:157 , ASP A:165 , ASP A:176 , ASP A:179	BINDING SITE FOR RESIDUE CA A 901
3	AC3	SOFTWARE	ASP A:155 , ASP A:157 , ASP A:179 , ASP A:388	BINDING SITE FOR RESIDUE CA A 902
4	AC4	SOFTWARE	GLU A:351 , ASP A:369 , SER A:370 , ARG A:372 , ASN A:373	BINDING SITE FOR RESIDUE CA A 903
5	AC5	SOFTWARE	ASP A:165 , ASP A:168 , GLU A:170	BINDING SITE FOR RESIDUE CA A 904
6	AC6	SOFTWARE	SER A:402 , GLY A:403 , ARG A:441	BINDING SITE FOR RESIDUE SO4 A 905
7	AC7	SOFTWARE	ARG A:495 , SER A:496 , LYS A:499 , LYS A:615	BINDING SITE FOR RESIDUE SO4 A 906
8	AC8	SOFTWARE	GLU A:511 , LYS A:525 , ASN A:528	BINDING SITE FOR RESIDUE SO4 A 907

(no "SS Bond" information available for 1WD9)

(no "Cis Peptide Bond" information available for 1WD9)

Asymmetric Unit (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053560	R	8	H	PADI4_HUMAN	Polymorphism	35381732	A	R	8	H
2	UniProt	VAR_053561	T	79	M	PADI4_HUMAN	Polymorphism	35809521	A	T	79	M
3	UniProt	VAR_020640	V	82	A	PADI4_HUMAN	Polymorphism	11203367	A	A	82	A
4	UniProt	VAR_027401	D	89	N	PADI4_HUMAN	Polymorphism	143187209	A	D	89	N
5	UniProt	VAR_027402	P	102	T	PADI4_HUMAN	Polymorphism	34309058	A	P	102	T
6	UniProt	VAR_020641	G	112	A	PADI4_HUMAN	Polymorphism	874881	A	A	112	A
7	UniProt	VAR_027404	M	164	T	PADI4_HUMAN	Polymorphism	11588132	A	M	164	T
8	UniProt	VAR_053562	D	260	N	PADI4_HUMAN	Polymorphism	35903413	A	D	260	N
9	UniProt	VAR_020642	S	275	F	PADI4_HUMAN	Polymorphism	1748020	A	S	275	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (9, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053560	R	8	H	PADI4_HUMAN	Polymorphism	35381732	A	R	8	H
2	UniProt	VAR_053561	T	79	M	PADI4_HUMAN	Polymorphism	35809521	A	T	79	M
3	UniProt	VAR_020640	V	82	A	PADI4_HUMAN	Polymorphism	11203367	A	A	82	A
4	UniProt	VAR_027401	D	89	N	PADI4_HUMAN	Polymorphism	143187209	A	D	89	N
5	UniProt	VAR_027402	P	102	T	PADI4_HUMAN	Polymorphism	34309058	A	P	102	T
6	UniProt	VAR_020641	G	112	A	PADI4_HUMAN	Polymorphism	874881	A	A	112	A
7	UniProt	VAR_027404	M	164	T	PADI4_HUMAN	Polymorphism	11588132	A	M	164	T
8	UniProt	VAR_053562	D	260	N	PADI4_HUMAN	Polymorphism	35903413	A	D	260	N
9	UniProt	VAR_020642	S	275	F	PADI4_HUMAN	Polymorphism	1748020	A	S	275	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1WD9)

Asymmetric Unit (16, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000375448	1b	ENSE00001883200	chr1:17634692-17634809	118	PADI4_HUMAN	1-31	31	1	A:4-31	28
1.2	ENST00000375448	2	ENSE00001268578	chr1:17657464-17657644	181	PADI4_HUMAN	31-91	61	1	A:31-91 (gaps)	61
1.3	ENST00000375448	3	ENSE00001044965	chr1:17660438-17660504	67	PADI4_HUMAN	92-114	23	1	A:92-114 (gaps)	23
1.6	ENST00000375448	6	ENSE00001044983	chr1:17662654-17662721	68	PADI4_HUMAN	114-136	23	1	A:114-136 (gaps)	23
1.7	ENST00000375448	7	ENSE00001044981	chr1:17664533-17664650	118	PADI4_HUMAN	137-176	40	1	A:137-176	40
1.8	ENST00000375448	8	ENSE00001044989	chr1:17666183-17666308	126	PADI4_HUMAN	176-218	43	1	A:176-217	42
1.9	ENST00000375448	9	ENSE00001268541	chr1:17668438-17668616	179	PADI4_HUMAN	218-277	60	1	A:225-277	53
1.10	ENST00000375448	10	ENSE00001044974	chr1:17668794-17668897	104	PADI4_HUMAN	278-312	35	1	A:278-312	35
1.11a	ENST00000375448	11a	ENSE00001044969	chr1:17672523-17672634	112	PADI4_HUMAN	312-349	38	1	A:312-349 (gaps)	38
1.12b	ENST00000375448	12b	ENSE00001044980	chr1:17674436-17674543	108	PADI4_HUMAN	350-385	36	1	A:350-385	36
1.14	ENST00000375448	14	ENSE00001044967	chr1:17681028-17681182	155	PADI4_HUMAN	386-437	52	1	A:386-437	52
1.15	ENST00000375448	15	ENSE00001044986	chr1:17682478-17682622	145	PADI4_HUMAN	437-485	49	1	A:437-485	49
1.16b	ENST00000375448	16b	ENSE00001044971	chr1:17682852-17682954	103	PADI4_HUMAN	486-520	35	1	A:486-515	30
1.17b	ENST00000375448	17b	ENSE00001044973	chr1:17685333-17685403	71	PADI4_HUMAN	520-543	24	1	A:523-543	21
1.18	ENST00000375448	18	ENSE00001044963	chr1:17685775-17685903	129	PADI4_HUMAN	544-586	43	1	A:544-586	43
1.19	ENST00000375448	19	ENSE00001467124	chr1:17690017-17690499	483	PADI4_HUMAN	587-663	77	1	A:587-663	77

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:603
 aligned with PADI4_HUMAN | Q9UM07 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:660
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663
          PADI4_HUMAN     4 GTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHGPPAKKKSTGSSTWPLDPGVEVTLTMKVASGSTGDQKVQISYYGPKTPPVKALLYLTGVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP 663
               SCOP domains d1wd9a2 A:4-112 Peptidylargini     ne deiminase Pa              d4, N-terminal domain                        d1wd9a1 A:11           3-293 Peptidylarginine deiminase Pad4, middle domain                                                                                                          d1wd9a3 A:294-663 P    eptidylarginine deimin       ase Pad4, catalytic C-terminal domain                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains PAD_N-1wd9A03 A:4-111                                                                                       -PAD_M-1wd9A0           2 A:113-273                                                                                                                               ----PAD-1wd9A01 A:278-663                                                                                                                                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .eeee......eeeeee....eeee.....-----.eeeee...eeeeee--------------.......eeeeee.........eeeeeee.--....eeeeeeeeeeeeeee......-----------............eee.............hhhhh....hhhhhhh.eeeeeeeee..hhhh.eeeeeeehhhhhh.eeeeee.-------.eeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...........eeeeeee.----hhhhhhhhhhhhhhh.eeeee.-------.hhhhheeeeeeee..eeeeeeee........hhhhhh......eeee........hhhhhhh.eee...eee..eee....eeeee...........hhhhhhhhhhhhhhh.eeee.......hhhh.eeeee..hhh.eeeeeeehhhhhhhhhhhhhh.....ee.-------.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..eee.hhh.eee........eee..eeeee.....ee..eehhhhhhhhhhhhhh.eeeee.....hhhhh.......eeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----H----------------------------------------------------------------------M--A------N------------T---------A---------------------------------------------------T-----------------------------------------------------------------------------------------------N--------------F---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:4-31      ------------------------------------------------------------Exon 1.3               ----------------------Exon 1.7  PDB: A:137-176                -----------------------------------------Exon 1.9  PDB: A:225-277 UniProt: 218-277 [INCOMPLETE]      Exon 1.10  PDB: A:278-312          -------------------------------------Exon 1.12b  PDB: A:350-385          Exon 1.14  PDB: A:386-437 UniProt: 386-437          ------------------------------------------------Exon 1.16b  PDB: A:486-515         -----------------------Exon 1.18  PDB: A:544-586 UniProt: 544-586 Exon 1.19  PDB: A:587-663 UniProt: 587-663                                    Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: A:31-91 (gaps) UniProt: 31-91                 ----------------------Exon 1.6               ---------------------------------------Exon 1.8  PDB: A:176-217 UniProt: 176-218  ---------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:312-349 (gaps)     ---------------------------------------------------------------------------------------Exon 1.15  PDB: A:437-485 UniProt: 437-485       ----------------------------------Exon 1.17b [INCOMPLETE] ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1wd9 A   4 GTLIRVTPEQPTHAVCVLGTLTQLDICSSA-----SFSINASPGVVVDIA--------------WPLDPGVEVTLTMKAASGSTGDQKVQISYY--KTPPVKALLYLTAVEISLCADITRT-----------QRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQAT-------CSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACS----EDFLKSVTTLAMKAKCKLTICP-------QWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLF-------QQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHAGTNVRRKPFSFKWWNMVP 663
                                    13        23        33     |  43        53         -    |   73        83        93   |  |103       113       123|        -  |    143       153       163       173       183       193       203       213   |     - |     233       243       253       263       273       283       293       303        |-   |   323       333    |    -  |    353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513 |     523       533       543       553       563       573       583       593       603       613       623       633       643       653       663
                                                        33    39            53             68                           97  |                     124         136                                                                              217     225                                                                                    312  317                  338     346                                                                                                                                                                      515     523                                                                                                                                            
                                                                                                                          100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 1WD9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GME (20)

Family: PAD (3)

Homo sapiens (Human) (3)

PAD-1wd9A01

A:278-663

Clan: no clan defined [family: PAD_M] (3)

Family: PAD_M (3)

Homo sapiens (Human) (3)

PAD_M-1wd9A02

A:113-273

Clan: no clan defined [family: PAD_N] (3)

Family: PAD_N (3)

Homo sapiens (Human) (3)

PAD_N-1wd9A03

A:4-111

Asymmetric Unit(hide GO term definitions)

Chain A (PADI4_HUMAN | Q9UM07)

molecular function
	GO:0016990	arginine deiminase activity	Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004668	protein-arginine deiminase activity	Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0036413	histone H3-R26 citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3.
	GO:0036414	histone citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0018101	protein citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0019827	stem cell population maintenance	The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wd9)

Biological Unit
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	1wd9
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	PADI4_HUMAN \| Q9UM07
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	3.5.3.15
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1wd8	THE SAME PROTEIN, CALCIUM FREE FORM
1wda	THE SAME PROTEIN WITH BENZOYL-L-ARGININE AMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

PROSITE Motifs (0, 0)

Exons (16, 16)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (3, 3)

Gene Ontology (22, 22)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File