8Q1K

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B (A, B)	5'-3' exonuclease PLD3	polymer	422	46945.8	2	UniProt (Q8IV08) Pfam (PF13918)	Homo sapiens (human)
2	C (C)	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G09609EN)
3	D, E (D, E)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
4	F (F)	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G55220VL)
5	G, H, I, P, Q... (A, B)	1,2-ETHANEDIOL	non-polymer		62.1	7	Chemie (EDO)
6	J, K, L, M, T... (A, B)	PHOSPHATE ION	non-polymer		95.0	8	Chemie (PO4)
7	N, O, X, Y (A, B)	MANGANESE (II) ION	non-polymer		54.9	4	Chemie (MN)
8	AA, Z (B, A)	water	water		18.0	1224	Chemie (HOH)

Sequence modifications

A, B: 72 - 490 (UniProt: Q8IV08)

PDB	External Database	Details
Ala 491	-	expression tag
Ala 492	-	expression tag
Gln 493	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	93891.5
Branched	Number of molecules	4
	Total formula weight	3319.0
Non-Polymers*	Number of molecules	19
	Total formula weight	1414.0
All*	Total formula weight	98624.5

*Water molecules are not included.