8YDS

Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	SARS-CoV-2 inhibiting peptide Ce59	polymer	39	4821.5	1		synthetic construct
2	B (B)	Spike protein S1	polymer	230	26270.2	1	UniProt (P0DTC2) Pfam (PF09408)	Severe acute respiratory syndrome coronavirus 2
3	C (C)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	1	In PDB GlyTouCan (G42666HT)
4	D, E (B)	GLYCEROL	non-polymer		92.1	2	Chemie (GOL)
5	F, G (A, B)	water	water		18.0	281	Chemie (HOH)

Sequence modifications

B: 333 - 526 (UniProt: P0DTC2)

PDB	External Database	Details
Arg 452	Leu 452	variant
Lys 478	Thr 478	variant
Ser 527	-	expression tag
Asn 528	-	expression tag
Ser 529	-	expression tag
Glu 530	-	expression tag
Asn 531	-	expression tag
Leu 532	-	expression tag
Tyr 533	-	expression tag
Phe 534	-	expression tag
Gln 535	-	expression tag
Gly 536	-	expression tag
Ser 537	-	expression tag
His 538	-	expression tag
His 539	-	expression tag
His 540	-	expression tag
His 541	-	expression tag
His 542	-	expression tag
His 543	-	expression tag
His 544	-	expression tag
His 545	-	expression tag
His 546	-	expression tag
His 547	-	expression tag
Gly 548	-	expression tag
Leu 549	-	expression tag
Asn 550	-	expression tag
Asp 551	-	expression tag
Ile 552	-	expression tag
Phe 553	-	expression tag
Glu 554	-	expression tag
Ala 555	-	expression tag
Gln 556	-	expression tag
Lys 557	-	expression tag
Ile 558	-	expression tag
Glu 559	-	expression tag
Trp 560	-	expression tag
His 561	-	expression tag
Glu 562	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	31091.7
Branched	Number of molecules	1
	Total formula weight	424.4
Non-Polymers*	Number of molecules	2
	Total formula weight	184.2
All*	Total formula weight	31700.3

*Water molecules are not included.