Structure of PDB 5rmk Chain B

Receptor sequence

>5rmkB (length=585) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCN
APGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSD
NVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGI
ATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFE
KGAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPT
LNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIV
YTACSHAAVDALCEKALKYLPIDKCSRIIPAVECFDKFKVNSTLEQYVFC
TVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAP
RTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYD
NKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK
AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNV
NRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIP

3D structure

• PDB: 5rmk Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
• Chain: B
• Resolution: 2.08 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

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	O2A	B	T552 A553 C556	T544 A545 C548
BS02	ZN	B	C16 C19 H33 H39	C15 C18 H32 H38
BS03	ZN	B	C5 C8 C26 C29	C4 C7 C25 C28
BS04	ZN	B	C50 C55 C72 H75	C49 C54 C71 H74
BS05	PO4	B	G285 G287 K288	G280 G282 K283
BS06	PO4	B	P284 K288 Q404 R443 G538 R567	P279 K283 Q396 R435 G530 R559

Gene Ontology

Molecular Function

• GO:0004386 helicase activity
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding

External links

• PDB: RCSB:5rmk, PDBe:5rmk, PDBj:5rmk
• PDBsum: 5rmk
• PubMed: 34381037
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)