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4YTG

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.

Functional Information from GO Data
ChainGOidnamespacecontents
A0004668molecular_functionprotein-arginine deiminase activity
A0009446biological_processputrescine biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue NA A 501
ChainResidue
AASP147
APHE148
AASP158
AHOH797

site_idAC2
Number of Residues7
Detailsbinding site for residue CYS A 502
ChainResidue
APHE460
ACYS462
ATYR378
APHE424
ATHR425
AGLY426
ALEU427

site_idAC3
Number of Residues5
Detailsbinding site for residue MET A 503
ChainResidue
ATRP127
AARG154
ATYR233
AARG504
AHOH724

site_idAC4
Number of Residues14
Detailsbinding site for residue ARG A 504
ChainResidue
ATRP127
AASP130
AARG152
AARG154
AGLY182
ATYR233
AILE234
AHIS236
AASP238
ATHR346
AALA351
AMET503
AHOH764
AHOH914

site_idAC5
Number of Residues7
Detailsbinding site for residue GOL A 505
ChainResidue
AILE149
ALYS176
AASN202
ASER204
AHOH798
AHOH804
AHOH824

site_idAC6
Number of Residues5
Detailsbinding site for residue GOL A 506
ChainResidue
AASP266
ATYR270
AHOH631
AHOH740
AHOH1001

site_idAC7
Number of Residues8
Detailsbinding site for residue GOL A 507
ChainResidue
AVAL55
AARG56
AGLY219
ALYS365
ATYR367
AHOH643
AHOH771
AHOH904

site_idAC8
Number of Residues8
Detailsbinding site for residue GOL A 508
ChainResidue
AASN247
ALYS248
AGLU283
APRO450
AASP456
AAZI512
AHOH815
AHOH869

site_idAC9
Number of Residues7
Detailsbinding site for residue GOL A 509
ChainResidue
ATYR399
ATYR422
ASER423
APHE424
ATHR425
ALEU427
AHOH674

site_idAD1
Number of Residues1
Detailsbinding site for residue CL A 510
ChainResidue
AASN49

site_idAD2
Number of Residues4
Detailsbinding site for residue AZI A 511
ChainResidue
AGLU232
AASN235
AHOH604
AHOH678

site_idAD3
Number of Residues5
Detailsbinding site for residue AZI A 512
ChainResidue
ALYS248
AGLU283
ATYR285
AASP456
AGOL508

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Amidino-cysteine intermediate","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

250359

PDB entries from 2026-03-11

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