Structure of PDB 3kum Chain G Binding Site BS01

Receptor Information

>3kum Chain G (length=354) Species: 226185 (Enterococcus faecalis V583)

MKIKQVHVRASKIKLKETFTIALGTIESADSAIVEIETEEGLVGYGEGGP
GIFITGETLAGTLETIELFGQAIIGLNPFNIEKIHEVMDKISAFAPAAKA
AIDIACYDLMGQKAQLPLYQLLGGYDNQVITDITLGIDEPNVMAQKAVEK
VKLGFDTLKIKVGTGIEADIARVKAIREAVGFDIKLRLDANQAWTPKDAV
KAIQALADYQIELVEQPVKRRDLEGLKYVTSQVNTTIMADESCFDAQDAL
ELVKKGTVDVINIKLMKCGGIHEALKINQICETAGIECMIGCMAEETTIG
ITAAAHLAAAQKNITRADLDATFGLETAPVTGGVSLEAKPLLELGEAAGL
GISH

Ligand information

• Ligand ID: ARG
• InChI: InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
• InChIKey: ODKSFYDXXFIFQN-BYPYZUCNSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: C(CC(C(=O)O)N)CNC(=[NH2+])N
  CACTVS 3.341: N[C@@H](CCCNC(N)=[NH2+])C(O)=O
  OpenEye OEToolkits 1.5.0: C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
  CACTVS 3.341: N[CH](CCCNC(N)=[NH2+])C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCCN\C(=[NH2+])N
• Formula: C6 H15 N4 O2
• Name: ARGININE
• PDB chain: 3kum Chain G Residue 355

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kum Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): F19 K161 C292 D318 D320
• Binding residue (residue number reindexed from 1): F19 K161 C292 D318 D320
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): F19 P50 F53 T134 K159 K161 D189 N191 E215 D240 E241 S242 N262 K264 G291 C292 M293 A317 D318 L319
• Catalytic site (residue number reindexed from 1): F19 P50 F53 T134 K159 K161 D189 N191 E215 D240 E241 S242 N262 K264 G291 C292 M293 A317 D318 L319
• Enzyme Commision number: 5.1.1.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016853 isomerase activity
• GO:0016854 racemase and epimerase activity
• GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
• GO:0046872 metal ion binding

Biological Process

• GO:0006518 peptide metabolic process
• GO:0009063 amino acid catabolic process

External links

• PDB: RCSB:3kum, PDBe:3kum, PDBj:3kum
• PDBsum: 3kum
• PubMed: 22392983
• UniProt: Q834W6|HYEP_ENTFA Hydrophobic dipeptide epimerase (Gene Name=EF_1511)