Structure of PDB 3njr Chain A Binding Site BS01

Receptor Information

>3njr Chain A (length=184) Species: 272942 (Rhodobacter capsulatus SB 1003)

MSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVS
VEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADL
PLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARH
GGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR

Ligand information

• Ligand ID: SAH
• InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
• InChIKey: ZJUKTBDSGOFHSH-WFMPWKQPSA-N
• SMILES:
  CACTVS 3.341: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
• Formula: C14 H20 N6 O5 S
• Name: S-ADENOSYL-L-HOMOCYSTEINE
• ChEMBL: CHEMBL418052
• DrugBank: DB01752
• ZINC: ZINC000004228232
• PDB chain: 3njr Chain A Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3njr An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): Q16 T18 G42 G43 S45 S47 E63 P64 R68 G110
• Binding residue (residue number reindexed from 1): Q17 T19 G43 G44 S46 S48 E64 P65 R69 G111
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.132: precorrin-6B C(5,15)-methyltransferase (decarboxylating).

Gene Ontology

Molecular Function

• GO:0008276 protein methyltransferase activity

Biological Process

• GO:0009236 cobalamin biosynthetic process

External links

• PDB: RCSB:3njr, PDBe:3njr, PDBj:3njr
• PDBsum: 3njr
• PubMed: 23042036
• UniProt: D5AV04