Structure of PDB 4ger Chain A Binding Site BS06

Receptor Information

>4ger Chain A (length=304) Species: 1406 (Paenibacillus polymyxa)

ATGTGKGVLGDTKSFTTTASGSSYQLKDTTRGNGVVTYTASNRQSIPGTI
LTDADNVWNDPAGVDAHTYAAKTYDYYKAKFGRNSIDGRGLQLRSTVHYG
SRYNNAFWNGSQMTYGDGDGSTFIAFSGDPDVVGHELTHGVTEYTSNLEY
YGESGALNEAFSDVIGNDIQRKNWLVGDDIYTPNIAGDALRSMSNPTLYD
QPDHYSNLYTGSSDNGGVHTNSGIINKAYYLLAQGGTFHGVTVNGIGRDA
AVQIYYSAFTNYLTSSSDFSNARAAVIQAAKDQYGANSAEATAAAKSFDA
VGVN

Ligand information

• Ligand ID: LYS
• InChI: InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
• InChIKey: KDXKERNSBIXSRK-YFKPBYRVSA-O
• SMILES:
  CACTVS 3.341: N[CH](CCCC[NH3+])C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCCC[NH3+]
  OpenEye OEToolkits 1.5.0: C(CC[NH3+])C[C@@H](C(=O)O)N
  CACTVS 3.341: N[C@@H](CCCC[NH3+])C(O)=O
  OpenEye OEToolkits 1.5.0: C(CC[NH3+])CC(C(=O)O)N
• Formula: C6 H15 N2 O2
• Name: LYSINE
• PDB chain: 4ger Chain A Residue 406

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ger Structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa.
• Resolution: 1.59 Å
• Binding residue (original residue number in PDB): N104 N105 F123 H219
• Binding residue (residue number reindexed from 1): N104 N105 F123 H219
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H135 E136 H139 Y150 E159 D214 H219
• Catalytic site (residue number reindexed from 1): H135 E136 H139 Y150 E159 D214 H219
• Enzyme Commision number: 3.4.24.28: bacillolysin.

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4ger, PDBe:4ger, PDBj:4ger
• PDBsum: 4ger
• PubMed: 23275160
• UniProt: P29148|NPRE_PAEPO Bacillolysin (Gene Name=npr)