9NWS

Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (C)	Sal-like protein 4	polymer	102	11493.8	1	UniProt (Q9UJQ4)	Homo sapiens (human)	Zinc finger protein 797,Zinc finger protein SALL4
2	B (A)	DNA damage-binding protein 1	polymer	860	96033.9	1	UniProt (Q16531)	Homo sapiens (human)	DDB p127 subunit,DNA damage-binding protein a,DDBa,Damage-specific DNA-binding protein 1,HBV X-associated protein 1,XAP-1,UV-damaged DNA-binding factor,UV-damaged DNA-binding protein 1,UV-DDB 1,XPE-binding factor,XPE-BF,Xeroderma pigmentosum group E-complementing protein,XPCe
3	C (B)	Protein cereblon	polymer	485	55144.6	1	UniProt (Q96SW2)	Homo sapiens (human)
4	D, E (C, B)	ZINC ION	non-polymer		65.4	2	Chemie (ZN)
5	F (B)	Mezigdomide	non-polymer		567.6	1	Chemie (QFC)

Sequence modifications

C: 392 - 449 (UniProt: Q9UJQ4)

PDB	External Database	Details
Met 348	-	expression tag
Asp 349	-	expression tag
Trp 350	-	expression tag
Ser 351	-	expression tag
His 352	-	expression tag
Pro 353	-	expression tag
Gln 354	-	expression tag
Phe 355	-	expression tag
Glu 356	-	expression tag
Lys 357	-	expression tag
Ser 358	-	expression tag
Ala 359	-	expression tag
Val 360	-	expression tag
Gly 361	-	expression tag
Leu 362	-	expression tag
Asn 363	-	expression tag
Asp 364	-	expression tag
Ile 365	-	expression tag
Phe 366	-	expression tag
Glu 367	-	expression tag
Ala 368	-	expression tag
Gln 369	-	expression tag
Lys 370	-	expression tag
Ile 371	-	expression tag
Glu 372	-	expression tag
Trp 373	-	expression tag
His 374	-	expression tag
Glu 375	-	expression tag
Gly 376	-	expression tag
Gly 377	-	expression tag
Gly 378	-	expression tag
Gly 379	-	expression tag
Ser 380	-	expression tag
Gly 381	-	expression tag
Glu 382	-	expression tag
Asn 383	-	expression tag
Leu 384	-	expression tag
Tyr 385	-	expression tag
Phe 386	-	expression tag
Gln 387	-	expression tag
Gly 388	-	expression tag
Gly 389	-	expression tag
Gly 390	-	expression tag
Arg 391	-	expression tag

A: 1 - 699 (UniProt: Q16531)

PDB	External Database	Details
Met -23	-	expression tag
Gly -22	-	expression tag
Ser -21	-	expression tag
Ser -20	-	expression tag
His -19	-	expression tag
His -18	-	expression tag
His -17	-	expression tag
His -16	-	expression tag
His -15	-	expression tag
His -14	-	expression tag
Ser -13	-	expression tag
Ala -12	-	expression tag
Val -11	-	expression tag
Asp -10	-	expression tag
Glu -9	-	expression tag
Asn -8	-	expression tag
Leu -7	-	expression tag
Tyr -6	-	expression tag
Phe -5	-	expression tag
Gln -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Gly -1	-	expression tag
Arg 0	-	expression tag

A: 706 - 1140 (UniProt: Q16531)

PDB	External Database	Details
Gly 700	-	linker
Asn 701	-	linker
Gly 702	-	linker
Asn 703	-	linker
Ser 704	-	linker
Gly 705	-	linker

B: 1 - 442 (UniProt: Q96SW2)

PDB	External Database	Details
Met -42	-	expression tag
Asp -41	-	expression tag
Tyr -40	-	expression tag
Lys -39	-	expression tag
Asp -38	-	expression tag
Asp -37	-	expression tag
Asp -36	-	expression tag
Asp -35	-	expression tag
Lys -34	-	expression tag
Ser -33	-	expression tag
Ala -32	-	expression tag
Val -31	-	expression tag
Asp -30	-	expression tag
Glu -29	-	expression tag
Asn -28	-	expression tag
Leu -27	-	expression tag
Tyr -26	-	expression tag
Phe -25	-	expression tag
Gln -24	-	expression tag
Gly -23	-	expression tag
Gly -22	-	expression tag
Gly -21	-	expression tag
Arg -20	-	expression tag
Gly -19	-	expression tag
Gly -18	-	expression tag
Ser -17	-	expression tag
Ala -16	-	expression tag
His -15	-	expression tag
Ile -14	-	expression tag
Val -13	-	expression tag
Met -12	-	expression tag
Val -11	-	expression tag
Asp -10	-	expression tag
Ala -9	-	expression tag
Tyr -8	-	expression tag
Lys -7	-	expression tag
Pro -6	-	expression tag
Thr -5	-	expression tag
Lys -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	162672.3
Non-Polymers*	Number of molecules	3
	Total formula weight	698.4
All*	Total formula weight	163370.7

*Water molecules are not included.