Structure of PDB 5ak8 Chain A Binding Site BS01

Receptor Information

>5ak8 Chain A (length=419) Species: 837 (Porphyromonas gingivalis)

SMNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASE
SQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLV
DFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSH
IAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAP
NKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYT
NSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGT
DALHARTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQ
CYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRK
ETYPFIGEPDPFKFTCMNE

Ligand information

• Ligand ID: ARG
• InChI: InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
• InChIKey: ODKSFYDXXFIFQN-BYPYZUCNSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: C(CC(C(=O)O)N)CNC(=[NH2+])N
  CACTVS 3.341: N[C@@H](CCCNC(N)=[NH2+])C(O)=O
  OpenEye OEToolkits 1.5.0: C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
  CACTVS 3.341: N[CH](CCCNC(N)=[NH2+])C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCCN\C(=[NH2+])N
• Formula: C6 H15 N4 O2
• Name: ARGININE
• PDB chain: 5ak8 Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ak8 Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.
• Resolution: 1.48 Å
• Binding residue (original residue number in PDB): W127 D130 R152 Y233 I234 H236 D238 T346 A351
• Binding residue (residue number reindexed from 1): W81 D84 R106 Y187 I188 H190 D192 T300 A305
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.5.3.-

Gene Ontology

Molecular Function

• GO:0004668 protein-arginine deiminase activity

Biological Process

• GO:0009446 putrescine biosynthetic process

External links

• PDB: RCSB:5ak8, PDBe:5ak8, PDBj:5ak8
• PDBsum: 5ak8
• PubMed: 26209657
• UniProt: Q9RQJ2|PAD_PORGI Peptidylarginine deiminase (Gene Name=PG_1424)