7ZSS

cryo-EM structure of D614 spike in complex with de novo designed binder

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C	Spike glycoprotein	polymer	1146	126639.5	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, P, h	de novo designed binder	polymer	79	8829.9	3	UniProt (Q9VKJ9) Pfam (PF21528) In PDB	Drosophila melanogaster (fruit fly)
3	E, F, G, H, I...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	7	In PDB GlyTouCan (G42666HT)
4	B, C, A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	32	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1146 (UniProt: P0DTC2)

PDB	External Database	Details
Gly 614	Asp 614	variant
Gly 682	Arg 682	engineered mutation
Ser 683	Arg 683	engineered mutation
Ser 685	Arg 685	engineered mutation
Pro 986	Lys 986	engineered mutation
Pro 987	Val 987	engineered mutation

D, P, h: 1 - 65 (UniProt: Q9VKJ9)

PDB	External Database	Details
Glu -5	-	expression tag
Thr -4	-	expression tag
Gly -3	-	expression tag
Ala -2	-	expression tag
Ser -1	-	expression tag
Ser 0	-	expression tag
Gln 12	Glu 370	engineered mutation
Phe 13	Lys 371	engineered mutation
His 15	Gln 373	engineered mutation
Gly 16	Ser 374	engineered mutation
Gln 17	Val 375	engineered mutation
Val 18	Glu 376	engineered mutation
Arg 20	Ala 378	engineered mutation
Ala 22	Lys 380	engineered mutation
Leu 23	Ala 381	engineered mutation
Gly 66	-	expression tag
Ser 67	-	expression tag
Glu 68	-	expression tag
Asn 69	-	expression tag
Leu 70	-	expression tag
Tyr 71	-	expression tag
Phe 72	-	expression tag
Gln 73	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	6
	Total formula weight	406408.2
Branched	Number of molecules	7
	Total formula weight	2970.8
Non-Polymers*	Number of molecules	32
	Total formula weight	7078.7
All*	Total formula weight	416457.7

*Water molecules are not included.