8FXB

SARS-CoV-2 XBB.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	L	S309 Light chain	polymer	214	23204.7	1		Homo sapiens
2	H	S309 Heavy chain	polymer	457	50163.3	1		Homo sapiens
3	A	Processed angiotensin-converting enzyme 2	polymer	648	74492.4	1	UniProt (Q9BYF1) Pfam (PF01401) In PDB	Homo sapiens (human)
4	E	Spike protein S1	polymer	249	28159.9	1	UniProt (P0DTC2) Pfam (PF09408) In PDB	Severe acute respiratory syndrome coronavirus
5	B	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		367.3	1	In PDB GlyTouCan (G86851RC)
6	A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	5	Chemie (NAG)

Sequence modifications

A: 19 - 615 (UniProt: Q9BYF1)

PDB	External Database	Details
Leu 616	-	expression tag
Val 617	-	expression tag
Pro 618	-	expression tag
Arg 619	-	expression tag
Gly 620	-	expression tag
Ser 621	-	expression tag
Ser 622	-	expression tag
Ala 623	-	expression tag
Trp 624	-	expression tag
Ser 625	-	expression tag
His 626	-	expression tag
Pro 627	-	expression tag
Gln 628	-	expression tag
Phe 629	-	expression tag
Glu 630	-	expression tag
Lys 631	-	expression tag
Gly 632	-	expression tag
Gly 633	-	expression tag
Gly 634	-	expression tag
Ser 635	-	expression tag
Gly 636	-	expression tag
Gly 637	-	expression tag
Gly 638	-	expression tag
Ser 639	-	expression tag
Gly 640	-	expression tag
Gly 641	-	expression tag
Ser 642	-	expression tag
Ala 643	-	expression tag
Trp 644	-	expression tag
Ser 645	-	expression tag
His 646	-	expression tag
Pro 647	-	expression tag
Gln 648	-	expression tag
Phe 649	-	expression tag
Glu 650	-	expression tag
Lys 651	-	expression tag
Gly 652	-	expression tag
Ser 653	-	expression tag
His 654	-	expression tag
His 655	-	expression tag
His 656	-	expression tag
His 657	-	expression tag
His 658	-	expression tag
His 659	-	expression tag
His 660	-	expression tag
His 661	-	expression tag
His 662	-	expression tag
His 663	-	expression tag
Gly 664	-	expression tag
Gly 665	-	expression tag
Gly 666	-	expression tag

E: 328 - 528 (UniProt: P0DTC2)

PDB	External Database	Details
Met 310	-	initiating methionine
Ala 311	-	expression tag
Arg 312	-	expression tag
Ala 313	-	expression tag
Trp 314	-	expression tag
Ile 315	-	expression tag
Phe 316	-	expression tag
Phe 317	-	expression tag
Leu 318	-	expression tag
Leu 319	-	expression tag
Cys 320	-	expression tag
Leu 321	-	expression tag
Ala 322	-	expression tag
Gly 323	-	expression tag
Arg 324	-	expression tag
Ala 325	-	expression tag
Leu 326	-	expression tag
Ala 327	-	expression tag
His 339	Gly 339	conflict
Thr 346	Arg 346	conflict
Ile 368	Leu 368	conflict
Phe 371	Ser 371	conflict
Pro 373	Ser 373	conflict
Phe 375	Ser 375	conflict
Ala 376	Thr 376	conflict
Asn 405	Asp 405	conflict
Ser 408	Arg 408	conflict
Asn 417	Lys 417	conflict
Lys 440	Asn 440	conflict
Pro 445	Val 445	conflict
Ser 446	Gly 446	conflict
Lys 460	Asn 460	conflict
Asn 477	Ser 477	conflict
Lys 478	Thr 478	conflict
Ala 484	Glu 484	conflict
Ser 486	Phe 486	conflict
Ser 490	Phe 490	conflict
Arg 498	Gln 498	conflict
Tyr 501	Asn 501	conflict
His 505	Tyr 505	conflict
Lys 529	-	expression tag
Ser 530	-	expression tag
Thr 531	-	expression tag
Gly 532	-	expression tag
Gly 533	-	expression tag
Leu 534	-	expression tag
Asn 535	-	expression tag
Asp 536	-	expression tag
Ile 537	-	expression tag
Phe 538	-	expression tag
Glu 539	-	expression tag
Ala 540	-	expression tag
Gln 541	-	expression tag
Lys 542	-	expression tag
Ile 543	-	expression tag
Glu 544	-	expression tag
Trp 545	-	expression tag
His 546	-	expression tag
Glu 547	-	expression tag
Gly 548	-	expression tag
Ser 549	-	expression tag
Gly 550	-	expression tag
His 551	-	expression tag
His 552	-	expression tag
His 553	-	expression tag
His 554	-	expression tag
His 555	-	expression tag
His 556	-	expression tag
His 557	-	expression tag
His 558	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	176020.2
Branched	Number of molecules	1
	Total formula weight	367.3
Non-Polymers*	Number of molecules	5
	Total formula weight	1106.0
All*	Total formula weight	177493.6

*Water molecules are not included.