Structure of PDB 4hnn Chain A Binding Site BS02

Receptor Information

>4hnn Chain A (length=307) Species: 29760 (Vitis vinifera)

SVDDIKSLRLITAIKTPYLPDGRFDLEAYDALVNMQIVDGAEGVIVGGTT
GEGQLMSWDEHIMLIGHTVNCFGGSIKVIGNTGSNSTREAIHATEQGFAV
GMHAALHINPYYGKTSLEGLVSHFESVLPMGPTVIYNVPSRTGQDIPPGV
IHTVAQSANLAGVKECVGNDRIKQYTDNRIVVWSGNDDQCHDAKWDYGAT
GVISVTSNLIPGLMRQLLFKGKNPSLNAKIMPLVNWLFEEPNPIGLNTAL
AQLGVVRPVFRLPYVPLPLAKRVEFVNIVKEIGRENFVGEKDVKVLDDDD
FILVGRY

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: 4hnn Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4hnn Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): N105 E109
• Binding residue (residue number reindexed from 1): N85 E89
• Annotation score: 2
• Binding affinity: MOAD: Kd=0.002mM
  PDBbind-CN: -logKd/Ki=5.70,Kd=2uM

Enzymatic activity

• Catalytic site (original residue number in PDB): T69 Y132 Y156 R161 K184 I223
• Catalytic site (residue number reindexed from 1): T49 Y112 Y136 R141 K164 I203
• Enzyme Commision number: 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.

Gene Ontology

Molecular Function

• GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
• GO:0016829 lyase activity

Biological Process

• GO:0009089 lysine biosynthetic process via diaminopimelate

External links

• PDB: RCSB:4hnn, PDBe:4hnn, PDBj:4hnn
• PDBsum: 4hnn
• PubMed: 23354837
• UniProt: D7U7T8