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4YTB

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) in complex with dipeptide Asp-Gln.

Functional Information from GO Data
ChainGOidnamespacecontents
A0004668molecular_functionprotein-arginine deiminase activity
A0009446biological_processputrescine biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues5
Detailsbinding site for residue NA A 501
ChainResidue
AASP147
APHE148
AASP158
AHOH806
AHOH890

site_idAC2
Number of Residues6
Detailsbinding site for residue ASP A 502
ChainResidue
AHOH796
AHOH970
ATRP127
AARG154
ATYR233
AGLN503

site_idAC3
Number of Residues14
Detailsbinding site for residue GLN A 503
ChainResidue
ATRP127
AASP130
AARG152
AARG154
ATYR233
AILE234
ATHR346
AASP347
ACYS351
AASP502
AHOH613
AHOH634
AHOH825
AHOH970

site_idAC4
Number of Residues10
Detailsbinding site for residue GOL A 504
ChainResidue
AASP266
AMET267
ATYR270
APRO455
AHOH633
AHOH703
AHOH716
AHOH792
AHOH842
AHOH949

site_idAC5
Number of Residues8
Detailsbinding site for residue GOL A 505
ChainResidue
ALYS176
AASN202
ASER204
AHOH673
AHOH692
AHOH741
AHOH751
AHOH872

site_idAC6
Number of Residues16
Detailsbinding site for residue GOL A 506
ChainResidue
ASER206
AGLN207
AALA208
AGLU283
ALYS459
AHOH605
AHOH649
AHOH679
AHOH699
AHOH709
AHOH745
AHOH761
AHOH794
AHOH963
AHOH1066
AHOH1122

site_idAC7
Number of Residues4
Detailsbinding site for residue PO4 A 507
ChainResidue
AALA390
ATHR391
AASN442
AHOH721

site_idAC8
Number of Residues8
Detailsbinding site for residue PO4 A 508
ChainResidue
APRO76
AMET77
AALA338
AHOH615
AHOH638
AHOH684
AHOH697
AHOH947

site_idAC9
Number of Residues4
Detailsbinding site for residue PO4 A 509
ChainResidue
AGLN212
ALYS215
AHOH710
AHOH757

site_idAD1
Number of Residues5
Detailsbinding site for residue PO4 A 510
ChainResidue
ATHR280
ALYS281
AHOH606
AHOH620
AHOH785

site_idAD2
Number of Residues3
Detailsbinding site for residue PO4 A 511
ChainResidue
AASN428
ALYS429
AGLU465

site_idAD3
Number of Residues2
Detailsbinding site for residue IMD A 512
ChainResidue
AARG70
APRO72

site_idAD4
Number of Residues8
Detailsbinding site for residue AZI A 514
ChainResidue
AHIS196
ATYR199
AVAL225
APRO455
AHOH603
AHOH625
AHOH917
AHOH955

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Amidino-cysteine intermediate => ECO:0000250
ChainResidueDetails
ACYS351

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PDB entries from 2024-05-01

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