Structure of PDB 5ud6 Chain D Binding Site BS03

Receptor Information

>5ud6 Chain D (length=299) Species: 280699 (Cyanidioschyzon merolae strain 10D)

KHFFGRVITALVTPFKLTGVEVDYGVAESLAAHLAENGSDAIIVAGTTGE
SATLTWSEEYELFRVVKSAVAGTKCRVIAGAGSNSTEEAIEATKKSAKLG
LDGTLQVVPYYNKPPQQGIMAHFRAIANAAPDLPMMLYNIPGRTGINMTA
ETSIKLAEMCPNIVALKEASGNLEQFARIRRATSPDFALYSGDDALTLPL
LSLGGNGVVSVASHFIGPEIQRMIEHFVDLGNPEEAFRIHCRYMDLFEAL
FVMANPIPAKAALRLLGWPVGPTRLPLTDITASAEQQLRQAMIAAGLLS

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: 5ud6 Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ud6 Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): A59 L61 W63 E66 Y117
• Binding residue (residue number reindexed from 1): A52 L54 W56 E59 Y110
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): T54 Y118 Y145 R150 K174 V216
• Catalytic site (residue number reindexed from 1): T47 Y111 Y138 R143 K167 V209
• 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:5ud6, PDBe:5ud6, PDBj:5ud6
• PDBsum: 5ud6
• UniProt: M1V4H9