Structure of PDB 1cvr Chain A Binding Site BS04

Receptor Information

>1cvr Chain A (length=432) Species: 837 (Porphyromonas gingivalis)

YTPVEEKENGRMIVIVAKKYEGDIKDFVDWKNQRGLRTEVKVAEDIASPV
TANAIQQFVKQEYEKEGNDLTYVLLVGDHKDIPAKITPGIKSDQVYGQIV
GNDHYNEVFIGRFSCESKEDLKTQIDRTIHYERNITTEDKWLGQALCIAS
AEGGPSADNGESDIQHENVIANLLTQYGYTKIIKCYDPGVTPKNIIDAFN
GGISLVNYTGHGSETAWGTSHFGTTHVKQLTNSNQLPFIFDVACVNGDFL
FSMPCFAEALMRAQKDGKPTGTVAIIASTIDQYWAPPMRGQDEMNEILCE
KHPNNIKRTFGGVTMNGMFAMVEKYKKDGENMLDTWTVFGDPSLLVRTLV
PTEMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAI
IKLNESIADETNLTLTVVGYNKVTVIKDVKVE

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: 1cvr Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1cvr Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): V100 D103 Y105 E107
• Binding residue (residue number reindexed from 1): V100 D103 Y105 E107
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): E152 H211 G212 C244
• Catalytic site (residue number reindexed from 1): E152 H211 G212 C244
• Enzyme Commision number: 3.4.22.37: gingipain R.

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity
• GO:0008234 cysteine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1cvr, PDBe:1cvr, PDBj:1cvr
• PDBsum: 1cvr
• PubMed: 10523290
• UniProt: P95493|CPG2_PORGI Gingipain R2 (Gene Name=rgpB)