Structure of PDB 2db3 Chain C

Receptor sequence

>2db3C (length=420) Species: 7227 (Drosophila melanogaster)

YIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSAD
LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLL
PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGI
VYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEA
DRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYV
FVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRG
ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASR
GLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI
AADLVKILEGSGQTVPDFLR

3D structure

• PDB: 2db3 Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
• Chain: C
• Resolution: 2.2 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	C	P326 T327 R328 G354 G355 T375 G377 R378 D381 R403 F409 E497 T498 K499 H520 G521 R528 T546 V548	P125 T126 R127 G153 G154 T174 G176 R177 D180 R202 F208 E296 T297 K298 H319 G320 R327 T345 V347
BS02	ANP	C	Y265 Q272 T291 G292 S293 G294 K295 T296 D554 R579 R582 V583	Y64 Q71 T90 G91 S92 G93 K94 T95 D353 R378 R381 V382

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003724 RNA helicase activity
• GO:0005524 ATP binding

External links

• PDB: RCSB:2db3, PDBe:2db3, PDBj:2db3
• PDBsum: 2db3
• PubMed: 16630817
• UniProt: P09052|VASA1_DROME ATP-dependent RNA helicase vasa (Gene Name=vas)