Structure of PDB 1nw5 Chain A Binding Site BS01

Receptor Information
>1nw5 Chain A (length=270) Species: 1063 (Cereibacter sphaeroides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTTRHVYDVCDCLDTLAKLPDDSVQLIICDPPYNIMLADWDDHMDYIGWA
KRWLAEAERVLSPTGSIAIFGGLQYQGEAGSGDLISIISHMRQNSKMLLA
NLIIWNYPNGMSAQRFFANRHEEIAWFAKTKKYFFDLDAVREPYDEETKA
AYMKDKRLNPESVEKGRNPTNVWRMSRLNGNSLERVGHPTQKPAAVIERL
VRALSHPGSTVLDFFAGSGVTARVAIQEGRNSICTDAAPVFKEYYQKQLT
FLRSYEIVEGAANFGAALQR
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain1nw5 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1nw5 Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding
Resolution2.05 Å
Binding residue
(original residue number in PDB)		D46 C47 D65 H223 T225 Q226 K227 F250 G252 S253 D271 A272
Binding residue
(residue number reindexed from 1)		D11 C12 D30 H188 T190 Q191 K192 F215 G217 S218 D236 A237
Annotation score5
Binding affinityMOAD: Kd=6.1uM
PDBbind-CN: -logKd/Ki=5.21,Kd=6.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D65 P66
Catalytic site (residue number reindexed from 1) D30 P31
Enzyme Commision number 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0008168 methyltransferase activity
GO:0008170 N-methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
Biological Process
GO:0009307 DNA restriction-modification system
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1nw5, PDBe:1nw5, PDBj:1nw5
PDBsum1nw5
PubMed12732637
UniProtP14751|MTR1_CERSP Type II methyltransferase M.RsrI (Gene Name=rsrIM)

[Back to BioLiP]