Structure of PDB 1im8 Chain B Binding Site BS02

Receptor Information
>1im8 Chain B (length=223) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDENVAEVFPDMIQRSVPGYSNIITAIGMLAERFVTADSNVYDLGCSRGA
ATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIR
HVEIKNASMVILNFTLQFLPPEDRIALLTKIYEGLNPNGVLVLSEKFRFE
DTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVMRTDSIETHKVRLK
NVGFSQVELWFQCFNFGSMIAVK
Ligand information
Ligand IDSAI
InChIInChI=1S/C14H20N6O5Se/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
InChIKeyUVSMMLABJBJNGH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C[Se]CCC(C(=O)O)N)O)O)N
CACTVS 3.341N[CH](CC[Se]C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CC[Se]CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341N[C@@H](CC[Se]C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[Se]CC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 Se
NameS-ADENOSYL-L-HOMOSELENOCYSTEINE
ChEMBL
DrugBankDB03423
ZINC
PDB chain1im8 Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1im8 Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		F19 F27 Y38 G63 S65 D88 N89 M93 D116 I117 N131 F136
Binding residue
(residue number reindexed from 1)		F1 F9 Y20 G45 S47 D70 N71 M75 D98 I99 N113 F118
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.3.-
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016743 carboxyl- or carbamoyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0002098 tRNA wobble uridine modification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1im8, PDBe:1im8, PDBj:1im8
PDBsum1im8
PubMed11746687
UniProtP43985|CMOA_HAEIN Carboxy-S-adenosyl-L-methionine synthase (Gene Name=cmoA)

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