Structure of PDB 6eom Chain A Binding Site BS02

Receptor Information

>6eom Chain A (length=524) Species: 880073 (Caldithrix abyssi DSM 13497)

LKRMIAQFAPTEIKYDHSLLDERKQKVVENLYRAAKIMDEIFLDQVYSKN
FEIREQLRASSDPLDQLRLEYFTIMFGPFDRLNHDKPFIGNTPKPKGANF
YPPDMTREEFENWLKAHPEDEAAFTSEFTVIRRQDGKLVAIPYSEYYKEY
LTRAADYLKKAAEFADNPSLKKYLQLRAEAFLNNDYYESDLAWMDLNDHT
IEVVIGPYEVYEDKLFNYKAAFEAFITLRDPVESAKLKKFVGYLDEMEKN
LPIPDAYKNFNRGSESPMVVVQEVFSAGDTKAGVQTLAFNLPNDERVREA
KGSKKVMLKNIHEAKFDKLLKPIAEKVLFAEQLPLVTFEGFFNHTLMHEI
SHGLGPGKIVLNGRQTEVKKELKETYSSIEECKADVLGMYNNLFMIEKGV
YPPEFEKQIYVTFLAGIFRTIRFGINEAHGAGNAVIFNYLLEKGAYQFDP
AAHRVKVNFEKIKDGVRDLANKVLTIQAQGDYMAAKNLLETYAVESEPIM
IMRARLQELPVDIKPIFQIEKELG

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: 6eom Chain A Residue 606

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6eom The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity.
• Resolution: 2.103 Å
• Binding residue (original residue number in PDB): V315 L318 K346 R450
• Binding residue (residue number reindexed from 1): V284 L287 K315 R419
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0008239 dipeptidyl-peptidase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6eom, PDBe:6eom, PDBj:6eom
• PDBsum: 6eom
• PubMed: 29420664
• UniProt: H1XW48