Structure of PDB 8x4o Chain B Binding Site BS01

Receptor Information

>8x4o Chain B (length=269) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KMRDRLFFLLSKYGIRPRDSIGQHFLIIEDVIEKAIETANVNENDVILEV
GPGLGFLTDELAKRAKKVYTIEIDQKIIEILKKEYSWNNVKIIQGDAVRV
EWPKFNKVVSNIPAKISSPFTFKLLKTDFERAVVMYQLEFALRMVAKPGS
RNYSRLSLMAQALGNVEIVMKIGKGAFYPRPKVDSALVLIEPRKDKIVLN
ENLVKALFQHRRKTVPRALKDSIHMLGVSKDEIRGIINNVPHSNKRVFQL
YPEEVKDIEEYLKKHGIIS

Ligand information

Ligand ID

MTA

InChI

InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1

InChIKey

WUUGFSXJNOTRMR-IOSLPCCCSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341	CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04	n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341	CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0	CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

Formula

C11 H15 N5 O3 S

Name

5'-DEOXY-5'-METHYLTHIOADENOSINE

PDB chain

8x4o Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8x4o Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.
Resolution	3.0 Å
Binding residue (original residue number in PDB)	I42 G43 Q44 G72 I92 E93 I94 D117 P134
Binding residue (residue number reindexed from 1)	I21 G22 Q23 G51 I71 E72 I73 D96 P113
Annotation score	4

External links

PDB	RCSB:8x4o, PDBe:8x4o, PDBj:8x4o
PDBsum	8x4o
PubMed	39146930
UniProt	O59487\|RSMA_PYRHO Probable ribosomal RNA small subunit methyltransferase A (Gene Name=rsmA)

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