Structure of PDB 3b1u Chain A

Receptor sequence

>3b1uA (length=628) Species: 9606 (Homo sapiens) [Search protein sequence]

GTLIRVTPEQPTHAVCVLGTLTQLDICSSAPETSFSINASPGVVVDITWP
LDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCA
DITRTGKQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQ
DMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATCSVVLGPKWPS
HYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVF
QDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLT
ICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVM
GPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCY
PSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRK
GFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTL
REHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPN
MVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFT
YHIRHGEVHCGTNVRRKPFSFKWWNMVP

3D structure

PDB

3b1u The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors

Chain

Resolution

2.1 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	D350 H471 D473 C645
Catalytic site (residue number reindexed from 1)	D315 H436 D438 C610
Enzyme Commision number	3.5.3.15: protein-arginine deiminase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	YFF	A	W347 D350 R374 V469 H471 D473 R639 H640 C645	W312 D315 R339 V434 H436 D438 R604 H605 C610	PDBbind-CN: -logKd/Ki=5.72,IC50=1.9uM
BS02	CA	A	Q349 E353 F407 L410 E411	Q314 E318 F372 L375 E376
BS03	CA	A	E351 D369 S370 N373	E316 D334 S335 N338
BS04	CA	A	N153 D155 D157 D165 D176 D179	N125 D127 D129 D137 D148 D151
BS05	CA	A	D155 D157 D179 D388	D127 D129 D151 D353
BS06	CA	A	D165 D168 E170	D137 D140 E142

Gene Ontology

	Molecular Function
GO:0004668	protein-arginine deiminase activity
GO:0005509	calcium ion binding
GO:0005515	protein binding
GO:0016787	hydrolase activity
GO:0042802	identical protein binding
GO:0046872	metal ion binding
GO:0140794	histone arginine deiminase activity
GO:0140795	histone H3R2 arginine deiminase activity
GO:0140796	histone H3R8 arginine deiminase activity
GO:0140797	histone H3R17 arginine deiminase activity
GO:0140798	histone H3R26 arginine deiminase activity

	Biological Process
GO:0006325	chromatin organization
GO:0006334	nucleosome assembly
GO:0006338	chromatin remodeling
GO:0019827	stem cell population maintenance
GO:0036211	protein modification process
GO:0043687	post-translational protein modification
GO:0045087	innate immune response

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0032991	protein-containing complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:3b1u, PDBe:3b1u, PDBj:3b1u
PDBsum	3b1u
PubMed	21882827
UniProt	Q9UM07\|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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