8Q1X

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	433	48190.1	2	UniProt (Q8IV08) Pfam (PF13918)	Homo sapiens (human)
2	C, E (C, E)	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		1073.0	2	In PDB GlyTouCan (G79306TC)
3	D, F (D, F)	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	G, H, X, Y (A, B)	THYMIDINE-5'-THIOPHOSPHATE	non-polymer		338.3	4	Chemie (PST)
5	I, J, Z (A, B)	PHOSPHATE ION	non-polymer		95.0	3	Chemie (PO4)
6	AA, BA, CA, DA, EA... (B, A)	1,2-ETHANEDIOL	non-polymer		62.1	15	Chemie (EDO)
7	GA, S (B, A)	MANGANESE (II) ION	non-polymer		54.9	2	Chemie (MN)
8	HA, IA, T, U (B, A)	SULFATE ION	non-polymer		96.1	4	Chemie (SO4)
9	JA, V (B, A)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
10	KA, LA (A, B)	water	water		18.0	1034	Chemie (HOH)

Sequence modifications

A, B: 61 - 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	96380.2
Branched	Number of molecules	4
	Total formula weight	2994.7
Non-Polymers*	Number of molecules	30
	Total formula weight	3111.8
All*	Total formula weight	102486.7

*Water molecules are not included.