Structure of PDB 6exf Chain D Binding Site BS02

Receptor Information

>6exf Chain D (length=346) Species: 239 (Flavobacterium sp.)

LTLEIPTSPLIIKITQQERNILSNVGNLLVKAFGNYENPDYIASLHLHAF
QLLPERITRILSQFGSDFSAEQYGAIVFQGLIEVDQDDLGPTPPNWQGAD
YGKLNKYGFICSLLHGAVPSKPVQYYAQRKGGGLLHAVIPDEKMAATQTG
SGSKTDLFVHTEDAFLSNQADFLSFLYLRNEERVPSTLYSIRSHGKMNPV
MKKLFEPIYQCPKDSGPTASVLYGNRELPFIRFDAAEQIFNENAGQTSEA
LGNLMDFWDEAKTLINSDYIPNSGDLIFVNNHLCAHGRSAFIAGQRIENG
EIIKCERRQMLRMMSKTSLIHIRSVTRTDDPYFIMEEHLGKIFDLD

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: 6exf Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6exf Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): T165 G166 H176 E178 D260
• Binding residue (residue number reindexed from 1): T149 G150 H160 E162 D234
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 1.14.11.-

Gene Ontology

Molecular Function

• GO:0016706 2-oxoglutarate-dependent dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

External links

• PDB: RCSB:6exf, PDBe:6exf, PDBj:6exf
• PDBsum: 6exf
• PubMed: 30410048
• UniProt: J3BZS6|LYS4O_FLASC L-lysine 4-hydroxylase (Gene Name=PMI10_03368)