11ZV

Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody (local refinement)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	PDCoV IL121_2014 receptor binding domain	polymer	175	19285.9	1	UniProt (F1NWE3) UniProt (W8Q9Y7)	Porcine deltacoronavirus	R-PTP-S,Chick receptor tyrosine phosphatase alpha,CRYP alpha,CRYPalpha
2	B (B)	RBD minibinder 11	polymer	176	20905.8	1		synthetic construct
3	C (C)	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		910.8	1	In PDB
4	D (D)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	1	In PDB
5	E, F (A, B)	water	water		18.0	46	Chemie (HOH)

Sequence modifications

A: 271 - 302 (UniProt: F1NWE3)

PDB	External Database	Details
Gly 272	Arg 2	conflict
Thr 300	Ser 30	conflict
Gly 301	Pro 31	conflict
Thr 302	Pro 32	conflict

A: 303 - 416 (UniProt: W8Q9Y7)

PDB	External Database	Details
Gly 417	-	linker
Gly 418	-	linker
Ser 419	-	linker
Gly 420	-	insertion
Leu 421	-	insertion
Asn 422	-	insertion
Asp 423	-	insertion
Ile 424	-	insertion
Phe 425	-	insertion
Glu 426	-	insertion
Ala 427	-	insertion
Gln 428	-	insertion
Lys 429	-	insertion
Ile 430	-	insertion
Glu 431	-	insertion
Trp 432	-	insertion
His 433	-	insertion
Glu 434	-	insertion
Gly 435	-	linker
Gly 436	-	linker
Ser 437	-	linker
His 438	-	expression tag
His 439	-	expression tag
His 440	-	expression tag
His 441	-	expression tag
His 442	-	expression tag
His 443	-	expression tag
His 444	-	expression tag
His 445	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	40191.7
Branched	Number of molecules	2
	Total formula weight	1335.2
All*	Total formula weight	41526.9

*Water molecules are not included.