Structure of PDB 6uk3 Chain B Binding Site BS01

Receptor Information

>6uk3 Chain B (length=475) Species: 1257118 (Acanthamoeba castellanii str. Neff)

TQTQTQPAGNAFQYEIRDISLAEFGRKEINLAEHEMPGLMQTREKYGAEQ
PLKGVRLAGSLHMTIQTAVLIETLQALGANVRWCSCNIFSTQDHAAAAIV
AAGTPVFAWKGETLEEYWECTWKTLLFPDDMGPQLIVDDGGDATLMVHRG
FYAEDNPSILDDDEGSEELAIVNKLLKRIQKEKPGYWHKIVPELKGVSEE
TTTGVHRLYEMMKEGKLLFPALNVNDSVTKSKFDNVYGCRHSLVDAIMRA
TDVMLSGKVACVLGYGDVGKGSAESLKGQGARVVVTEVDPICALQACMAG
YEVVRIEDVLDKAEIFVTTTGNCDIIRIEHMEKMRHNAIVCNIGHFDNEI
QVKALKEFPGIKRIEIKPQVDQFVFPDGHAIVLLAEGRLVNLGCATGHPS
FVMSNSFTNQTLAQISLWKEKYELGVYTLPKKLDEEVARLHLEKLGAKLT
VLTDKQAKYLGIAKDGPYKPDHYRY

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 6uk3 Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6uk3 Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): T203 T204 T205 N237 G268 D269 V270 E289 V290 T322 N324 I327 I345 G346 N393 H400
• Binding residue (residue number reindexed from 1): T201 T202 T203 N235 G266 D267 V268 E287 V288 T320 N322 I325 I343 G344 N391 H398
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): H64 S87 S92 D141 E202 N227 K232 D236 N237 C241 H347 H400 S408 Q412
• Catalytic site (residue number reindexed from 1): H62 S85 S90 D139 E200 N225 K230 D234 N235 C239 H345 H398 S406 Q410
• Enzyme Commision number: 3.13.2.1: adenosylhomocysteinase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004013 adenosylhomocysteinase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0006730 one-carbon metabolic process
• GO:0033353 S-adenosylmethionine cycle

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6uk3, PDBe:6uk3, PDBj:6uk3
• PDBsum: 6uk3
• UniProt: L8H6B5