5PMK

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 178)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Lysine-specific demethylase 4D	polymer	364	42050.5	1	UniProt (Q6B0I6) Pfam (PF02375) Pfam (PF02373)	Homo sapiens (Human)	JmjC domain-containing histone demethylation protein 3D,Jumonji domain-containing protein 2D
2	B (A)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)
3	C (A)	NICKEL (II) ION	non-polymer		58.7	1	Chemie (NI)
4	D (A)	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)
5	E (A)	N-OXALYLGLYCINE	non-polymer		147.1	1	Chemie (OGA)
6	F, G, H, I, J... (A)	1,2-ETHANEDIOL	non-polymer		62.1	8	Chemie (EDO)
7	N, O, P (A)	SULFATE ION	non-polymer		96.1	3	Chemie (SO4)
8	Q (A)	water	water		18.0	441	Chemie (HOH)

Sequence modifications

A: 1 - 342 (UniProt: Q6B0I6)

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

Contents of the asymmetric unit

Polymers	Number of chains	1
	Total formula weight	42050.5
Non-Polymers*	Number of molecules	15
	Total formula weight	1080.2
All*	Total formula weight	43130.8

*Water molecules are not included.