8YDW

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE

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 CeSPIACE	polymer	39	4721.5	1		synthetic construct
2	B (B)	Spike protein S1	polymer	230	26204.3	1	UniProt (P0DTC2) Pfam (PF09408)	Severe acute respiratory syndrome coronavirus 2
3	C (B)	GLYCEROL	non-polymer		92.1	1	Chemie (GOL)
4	D (B)	SODIUM ION	non-polymer		23.0	1	Chemie (NA)
5	E, F (A, B)	water	water		18.0	73	Chemie (HOH)

Sequence modifications

B: 333 - 526 (UniProt: P0DTC2)

PDB	External Database	Details
His 339	Gly 339	variant
Thr 346	Arg 346	variant
Ile 368	Leu 368	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Ala 376	Thr 376	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Pro 445	Val 445	variant
Ser 446	Gly 446	variant
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Pro 486	Phe 486	variant
Ser 490	Phe 490	variant
Arg 493	Gln 493	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	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	30925.7
Non-Polymers*	Number of molecules	2
	Total formula weight	115.1
All*	Total formula weight	31040.8

*Water molecules are not included.