Structure of PDB 6i9a Chain B

Receptor sequence
>6i9aB (length=453) Species: 837 (Porphyromonas gingivalis) [Search protein sequence]
DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEA
EVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKV
TDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYL
EKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGC
YSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCI
TAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFG
VQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGA
HYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYV
AISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQI
QVG
3D structure
PDB6i9a Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor.
ChainB
Resolution1.2 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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.
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 CA B D337 D339 F341 E343 D109 D111 F113 E115
BS02 CA B D313 F482 E491 D85 F254 E263
BS03 H8E B A443 H444 G445 A451 N475 C477 I478 N510 S511 Y512 W513 D516 H575 A215 H216 G217 A223 N247 C249 I250 N282 S283 Y284 W285 D288 H347
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:6i9a, PDBe:6i9a, PDBj:6i9a
PDBsum6i9a
PubMed30894633
UniProtQ51817|KGP83_PORGN Lys-gingipain W83 (Gene Name=kgp)

[Back to BioLiP]