6PKI

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S C230S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)

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, D (A, B, C, D)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	polymer	309	34048.8	4	UniProt (F1QSF9) Pfam (PF09992)	Danio rerio (Zebrafish)
2	E, F, K, L, Q... (A, B, C, D)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	8	Chemie (NAG)
3	G, M, S, Y (A, B, C, D)	2-acetamido-2-deoxy-alpha-D-glucopyranose	non-polymer		221.2	4	Chemie (NDG)
4	H, N, T, U, Z (A, B, C, D)	6-O-phosphono-alpha-D-mannopyranose	non-polymer		260.1	5	Chemie (M6P)
5	I (A)	PENTAETHYLENE GLYCOL	non-polymer		238.3	1	Chemie (1PE)
6	J, O, P, V (A, B, C)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
7	AA, BA, CA, DA (A, B, C, D)	water	water		18.0	625	Chemie (HOH)

Sequence modifications

A, B, C, D: 39 - 336 (UniProt: F1QSF9)

PDB	External Database	Details
Asp 28	-	expression tag
Arg 29	-	expression tag
His 30	-	expression tag
His 31	-	expression tag
His 32	-	expression tag
His 33	-	expression tag
His 34	-	expression tag
His 35	-	expression tag
Gly 36	-	expression tag
Ser 37	-	expression tag
Gly 38	-	expression tag
Ser 56	Cys 75	engineered mutation
Ser 230	Cys 249	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	136195.2
Non-Polymers*	Number of molecules	22
	Total formula weight	4335.3
All*	Total formula weight	140530.5

*Water molecules are not included.