Structure of PDB 6vjb Chain A Binding Site BS02

Receptor Information

>6vjb Chain A (length=1346) Species: 1314 (Streptococcus pyogenes)

SLPPVNTDVHDWVKTKGAWDKGYKGQGKVVAVIATGIDPAHQSMRISDVS
TAKVKSKEDMLARQKAAGINYGSWINDKVVFAHNYVENSDNIKENQDTKY
ESHGMHVTGIVAGNSKEAAATGERFLGIAPEAQVMFMRVFANDIMGSAES
LFIKAIEDAVALGADVINLSLGTANGAQLSGSKPLMEAIEKAKKAGVSVV
VAAGNERVYGSDHDDPLATNPDYGLVGSPSTGRTPTSVAAINSKWVIQRL
MTVKELENRADLNHGKAIYSESVDFKDIKDSLGQFAYVKESTDAGIALIE
RDPNKTYDEMIALAKKHGLGVLIFNNKPGQSNRSMRFISHEFGKAMSQLN
GNGTGSLEFDSVVSKAPSQKGNEMNHFSNWGLTSDGYLKPDITAPGGDIY
STYNDNHYGSQTGTAMASPQIAGASLLVKQYLEKTQPNLPKEKIADIVKN
LLMSNAQIHVNPETKTTTSPRQQGAGLLNIDGAVTSGLYVTGKDNYGSIS
LGNITDTMTFDVTVHNLSNKDKTLRYDTELLTDHVDPQKGRFTLTSHSLK
TYQGGEVTVPANGKVTVRVTMDVSQFTKELTKQMPNGYYLEGFVRFRDSQ
DDQLNRVNIPFVGFKGQFENLAVAEESIYRLKSQGKTGFYFDESGPKDDI
YVGKHFTGLVTLGSETNVSTKTISDNGLHTLGTFKNADGKFILEKNAQGN
PVLAISPNGDNNQDFAAFKGVFLRKYQGLKASVYHASDKEHKNPLWVSPE
SFKGDKNFNSDIRFAKSTTLLGTAFSGKSLTGAELPDGHYHYVVSYYPDV
VGAKRQEMTFDMILDRQKPVLSQATFDPETNRFKPEPLKDRGLAGVRKDS
VFYLERKDNKPYTVTINDSYKYVSVEDNKTFVERQADGSFILPLDKAKLG
DFYYMVEDFAGNVAIAKLGDHLPTPIKLKLTDGNYQTKETLKDNLEMTQS
DTGLVTNQAQLAVVHRNQPQSQLTKMNQDFFISPNEDGNKDFVAFKNNVY
NDLTVNVYAKDDHQKQTPIWSSQAGASVSAIESTAWYGITARGSKVMPGD
YQYVVTEHQKQYTISVNDKKPMITQGRFDTINGVDHFTPDKTLDSSGIVR
EEVFYLAKKNGRKFDVTEGITVSDNKVYIPKNPDGSYTISKRDGVTLSDY
YYLVEDRAGNVSFATLRDLKAVGKDKAVVNFGLDLFTYLVRDADGKPIEN
LEYYNNSGNSLILPYGKYTVELLTYDTNAAKLESDKIVSFTLSADNNFQQ
VTFKITMLATSQITAHFDHLLPEGSRVSLKTAQDQLIPLEQSLYVPKAYG
KTVQEGTYEVVVSLPKGYRIEGNTKVNTLPNEVHELSLRLVKVGDA

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: 6vjb Chain A Residue 1706

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vjb Structure, dynamics and immunogenicity of a catalytically inactive CXC chemokine-degrading protease SpyCEP from Streptococcus pyogenes.
• Resolution: 2.24 Å
• Binding residue (original residue number in PDB): S908 N910 D912 N914 D916
• Binding residue (residue number reindexed from 1): S706 N708 D710 N712 D714
• 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
• GO:0046872 metal ion binding

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005618 cell wall
• GO:0016020 membrane

External links

• PDB: RCSB:6vjb, PDBe:6vjb, PDBj:6vjb
• PDBsum: 6vjb
• PubMed: 32257048
• UniProt: Q9A180