Structure of PDB 4rbm Chain A Binding Site BS05

Receptor Information
>4rbm Chain A (length=452) Species: 837 (Porphyromonas gingivalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEA
EVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKV
TDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYL
EKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGC
YSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCI
TAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFG
VQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGA
HYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYV
AISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQI
QV
Ligand information
Ligand IDAZI
InChIInChI=1S/N3/c1-3-2/q-1
InChIKeyIVRMZWNICZWHMI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341
OpenEye OEToolkits 1.5.0		[N-]=[N+]=[N-]
FormulaN3
NameAZIDE ION
ChEMBLCHEMBL79455
DrugBank
ZINC
PDB chain4rbm Chain A Residue 711 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4rbm Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H234 G235 L237
Binding residue
(residue number reindexed from 1)		H6 G7 L9
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D388 H444 G445 C477
Catalytic site (residue number reindexed from 1) D160 H216 G217 C249
Enzyme Commision number 3.4.22.47: gingipain K.
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rbm, PDBe:4rbm, PDBj:4rbm
PDBsum4rbm
PubMed25266723
UniProtQ51817|KGP83_PORGN Lys-gingipain W83 (Gene Name=kgp)

[Back to BioLiP]