Structure of PDB 2gk6 Chain B Binding Site BS02

Receptor Information
>2gk6 Chain B (length=602) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRI
AYFTLPLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSV
GAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHE
VEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKT
VTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR
EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDLSSADEKRYRALKRTAE
RELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG
AKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR
MHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQG
QEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYL
VQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRIGFLNDPRRL
NVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRES
LM
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2gk6 Chain B Residue 1820 [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]
PDB2gk6 Structural and functional insights into the human Upf1 helicase core
Resolution2.4 Å
Binding residue
(original residue number in PDB)		P469 D470 Q475 G497 K498 T499 V500 Y702
Binding residue
(residue number reindexed from 1)		P170 D171 Q176 G198 K199 T200 V201 Y399
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity

View graph for
Molecular Function
External links
PDB RCSB:2gk6, PDBe:2gk6, PDBj:2gk6
PDBsum2gk6
PubMed17159905
UniProtQ92900|RENT1_HUMAN Regulator of nonsense transcripts 1 (Gene Name=UPF1)

[Back to BioLiP]