Structure of PDB 2xgj Chain B Binding Site BS02

Receptor Information

>2xgj Chain B (length=777) Species: 4932 (Saccharomyces cerevisiae)

HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGES
VLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEF
GDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHY
MRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHI
VYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISKGDIY
KIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFN
NAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGF
LKVLFATETFSIGPAKTVVFTSVVSGGEYIQMSGRAGRRGLDDRGIVIMM
IDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHS
FFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYRE
DVRQVVTHPANALPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRL
EELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCT
PNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQ
ERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHE
LMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIG
NSSLKEKMEAVLKLIHRDIVSAGSLYL

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 2xgj Chain B Residue 2074

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2xgj Structural Analysis Reveals the Characteristic Features of Mtr4, a Dexh Helicase Involved in Nuclear RNA Processing and Surveillance.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): F148 Q154 T173 S174 G176 K177 T178 R547
• Binding residue (residue number reindexed from 1): F32 Q38 T57 S58 G60 K61 T62 R389
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0003729 mRNA binding
• GO:0003824 catalytic activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008143 poly(A) binding
• GO:0016491 oxidoreductase activity
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0034458 3'-5' RNA helicase activity

Biological Process

• GO:0000292 RNA fragment catabolic process
• GO:0000460 maturation of 5.8S rRNA
• GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006397 mRNA processing
• GO:0006401 RNA catabolic process
• GO:0016075 rRNA catabolic process
• GO:0034475 U4 snRNA 3'-end processing
• GO:0034476 U5 snRNA 3'-end processing
• GO:0071028 nuclear mRNA surveillance
• GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing
• GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
• GO:0071038 TRAMP-dependent tRNA surveillance pathway
• GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process
• GO:0071051 poly(A)-dependent snoRNA 3'-end processing

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0031499 TRAMP complex

External links

• PDB: RCSB:2xgj, PDBe:2xgj, PDBj:2xgj
• PDBsum: 2xgj
• PubMed: 20566885
• UniProt: P47047|MTR4_YEAST ATP-dependent RNA helicase DOB1 (Gene Name=MTR4)