Structure of PDB 3b1t Chain A

Receptor sequence

>3b1tA (length=624) Species: 9606 (Homo sapiens) [Search protein sequence]

GTLIRVTPEQPTHAVCVLGTLTQLDICSSAPTSFSINASPGVVVDITWPL
DPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCAD
ITRTGKQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQD
MSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATCSVVLGPKWPSH
YLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQ
DSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTI
CPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMG
PDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYP
SNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKG
FRLLLASPRSCYKLFQEQQNEGHGEALLFEGKKQQKIKNILSNKTLREHN
SFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNM
LVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIR
HGEVHCGTNVRRKPFSFKWWNMVP

3D structure

PDB

3b1t 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

2.5 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)	D314 H435 D437 C606
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	YCL	A	W347 D350 R374 V469 H471 D473 R639 C645	W311 D314 R338 V433 H435 D437 R600 C606	PDBbind-CN: -logKd/Ki=5.66,IC50=2.2uM
BS02	CA	A	Q349 E353 F407 L410 E411	Q313 E317 F371 L374 E375
BS03	CA	A	E351 D369 S370 N373	E315 D333 S334 N337
BS04	CA	A	N153 D155 D157 D165 D176 D179	N124 D126 D128 D136 D147 D150
BS05	CA	A	D155 D157 D179 D388	D126 D128 D150 D352
BS06	CA	A	D165 D168 E170	D136 D139 E141

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

View graph for
Cellular Component

External links

PDB	RCSB:3b1t, PDBe:3b1t, PDBj:3b1t
PDBsum	3b1t
PubMed	21882827
UniProt	Q9UM07\|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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