Structure of PDB 3h5y Chain A

Receptor sequence

>3h5yA (length=474) Species: 11983 (Norwalk virus)

KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVK
GGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKW
SFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEG
KNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMD
ELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAV
LAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPC
TSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLD
PEKLTAKLKEYGLKPTRPPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQS
SILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKIS
KLVIAELDFYVPRQEPMFRWMRFS

3D structure

• PDB: 3h5y Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site.
• Chain: A
• Resolution: 1.77 Å

Enzymatic activity

• Enzyme Commision number: 3.4.22.66: calicivirin.

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	A	S306 Y341 D344 L391 R392 L406 S410 R413 Q414 R419	S302 Y337 D340 L382 R383 L397 S401 R404 Q405 R410
BS02	rna	A	P20 T117 S118 K127 A164 K166 L184 G186 M192 K207 G218 M219 N220 G301 Y341 N422 Q439	P16 T113 S114 K123 A160 K162 L180 G182 M188 K203 G214 M215 N216 G297 Y337 N413 Q430
BS03	MN	A	D242 D343 D344	D238 D339 D340
BS04	MN	A	D242 Y243 D343	D238 Y239 D339
BS05	MN	A	A241 D242 D344	A237 D238 D340
BS06	MN	A	D99 E205 H209	D95 E201 H205
BS07	CTP	A	R182 D242 Y243 R245 W246 D247 S300 D343	R178 D238 Y239 R241 W242 D243 S296 D339

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0004386 helicase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:3h5y, PDBe:3h5y, PDBj:3h5y
• PDBsum: 3h5y
• PubMed: 19426741
• UniProt: Q70ET3