Structure of PDB 2pb5 Chain A Binding Site BS01

Receptor Information
>2pb5 Chain A (length=265) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKL
IGKEIRVLSREDVELNFENIVLPMAKENDVAFLTPGDPLVATTHAELRIR
AKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYD
VIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDD
TLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYL
VEIAGAPREILRVNV
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 chain2pb5 Chain A Residue 501 [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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PDB2pb5 Crystal structure of PH0725 from Pyrococcus horikoshii OT3
Resolution2.1 Å
Binding residue
(original residue number in PDB)		T36 S37 G86 D87 V90 S115 I116 F165 L166 R208 A209 P233 H234 I235
Binding residue
(residue number reindexed from 1)		T36 S37 G86 D87 V90 S115 I116 F165 L166 R208 A209 P233 H234 I235
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:2pb5, PDBe:2pb5, PDBj:2pb5
PDBsum2pb5
PubMed
UniProtO58456|DPHB_PYRHO Diphthine synthase (Gene Name=dphB)

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