Structure of PDB 2ek3 Chain A Binding Site BS01

Receptor Information
>2ek3 Chain A (length=264) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLI
GKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRA
KRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDV
IKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDT
LVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLV
EIAGAPREILRVNV
Ligand information
Ligand IDSAH
InChIInChI=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
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain2ek3 Chain A Residue 301 [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]
PDB2ek3 Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L3M)
Resolution2.8 Å
Binding residue
(original residue number in PDB)		L10 T36 S37 G86 D87 V90 A91 S115 I116 F165 L166 A209 P233 H234 I235
Binding residue
(residue number reindexed from 1)		L9 T35 S36 G85 D86 V89 A90 S114 I115 F164 L165 A208 P232 H233 I234
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.98: diphthine synthase.
Gene Ontology
Molecular Function
GO:0004164 diphthine synthase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0017183 protein histidyl modification to diphthamide
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ek3, PDBe:2ek3, PDBj:2ek3
PDBsum2ek3
PubMed
UniProtO58456|DPHB_PYRHO Diphthine synthase (Gene Name=dphB)

[Back to BioLiP]