Structure of PDB 5rma Chain A

Receptor sequence

>5rmaA (length=572) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVC
NAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKVTDFNA
IATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVL
SDRELHLSWEVGKPRPPLNRNYVFTGYQIGEYTFEKDAVVYRGTTTYKLN
VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQ
KVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEK
ALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADI
VVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE
YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQ
CFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNA
VASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKV
GILCIMSDRDLYDKLQFTSLEI

3D structure

• PDB: 5rma Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
• Chain: A
• Resolution: 1.89 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	ZN	A	C50 C55 C72 H75	C50 C55 C72 H75
BS02	ZN	A	C16 C19 H33 H39	C16 C19 H33 H39
BS03	ZN	A	C5 C8 C29	C5 C8 C29
BS04	PO4	A	G285 G287 K288	G265 G267 K268
BS05	PO4	A	P284 K288 Q404 R443 G538 R567	P264 K268 Q384 R423 G518 R547

Gene Ontology

Molecular Function

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

External links

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