Structure of PDB 5xyr Chain A Binding Site BS03

Receptor Information

>5xyr Chain A (length=1380) Species: 1314 (Streptococcus pyogenes)

LPPVNTDIHDWVKTKGAWDKGYKGQGKVVAVIDTGIDPAHQSMRISDVST
AKVKSKEDMLARQKAAGINYGSWINDKVVFAHNYVENSDNIKENQDTKYE
SHGMHVTGIVAGNSKEAAATGERFLGIAPEAQVMFMRVFANDVMGSAESL
FIKAIEDAVALGADVINLSLGTANGAQLSGSKPLMEAIEKAKKAGVSVVV
AAGNERVYGSDHDDPLATNPDYGLVGSPSTGRTPTSVAAINSKWVIQRLM
TVEELEKRADLNHGKAIYSESVDFKNIKDSHQFAYVKESTDAGYNAQDVK
GKIALIERDPNKTYDEMIALAKKHGALGVLIFNNKPGQSNRIPSAFISHE
FGKAMSQLNGNTGSLEFDSVVSKAPSQKGNEMNHFSNWGLTSDGYLKPDI
TAPGGDIYSTYNDNHYGSQTGTSMASPQIAGASLLVKQYLEKTQPNLPKE
KIADIVKNLLMSNAQIHVNPETKTTTSPRQQGAGLLNIDGAVTSGLYVTG
KDNYGSISLGNITDTMTFDVTVHNLSNKDKTLRYDTELLTDHVDPQKGRF
TLTSRSLKTYQGGEVTVPANGKVTVRVTMDVSQFTKELTKQMPNGYYLEG
FVRFRDSQDDQLNRVNIPFVGFKGQFENLAVAEESIYRLKSQGKTGFYFD
ESGPKDDIYVGKHFTGLVTLGSETNVSTKTISDNGLHTLGTFKNADGKFI
LEKNAQGNPVLAISPNGDNNQDFAAFKGVFLRKYQGLKASVYHASDKEHK
NPLWVSPESFKGDKNFNSDIRFAKSTTLLGTAFSGKSLTGAELPDGYYHY
VVSYYPDVVGAKRQEMTFDMILDRQKPVLSQATFDPETNRFKPEPLKDRG
LAGVRKDSVFYLERKDNKPYTVTINDSYKYVSVEDNKTFVERQADGSFIL
PLDKAKLGDFYYMVEDFAGNVAIAKLGDHLPQTLGKTPIKLKLTDGNYQT
KETLKDNLEMTQSDTGLVTNQAQLAVVHRNQPQSQLTKMNQDFFISPNED
GNKDFVAFKGLENNVYNDLTVNVYAKDDHQKQTPIWSSQAGAGASAIEST
AWYGITARGSKVMPGDYQYVVTYRDEHGKEHQKQYTISVNDKKPMITQGR
FDTINGVDHFTPDKTKALGSSGIVREEVFYLAKKNGRKFDVTEGKDGITV
SDNKVYIPKNPDGSYTISKRDGVTLSDYYYLVEDRAGNVSFATLRDLKAV
GKDKAVVNFGLDLPVPEDKQIVNFTYLVRDADGKPIENLEYYNNSGNSLI
LPYGKYTVELLTYDTNAAKLESDKIVSFTLSADNNFQQVTFKMTMLATSQ
ITAHFDHLLPEGSRVSLKTAQGQLIPLEQSLYVPKAYGKTVQEGTYEVVV
SLPKGYRIEGNTKVNTLPNEVHELSLRLVK

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 5xyr Chain A Residue 1704

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xyr Structure of ScpC, a virulence protease fromStreptococcus pyogenes, reveals the functional domains and maturation mechanism.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): S908 N910 D912 N914 D916
• Binding residue (residue number reindexed from 1): S714 N716 D718 N720 D722
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.4.21.110: C5a peptidase.

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity
• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005618 cell wall
• GO:0016020 membrane

External links

• PDB: RCSB:5xyr, PDBe:5xyr, PDBj:5xyr
• PDBsum: 5xyr
• PubMed: 30049896
• UniProt: Q3HV58