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 | 5'-3' exonuclease PLD3 | polymer | 433 | 48190.1 | 2 | UniProt (Q8IV08) Pfam (PF13918) In PDB | Homo sapiens (human) | |
2 | 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 | 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 | A, B | THYMIDINE-5'-THIOPHOSPHATE | non-polymer | 338.3 | 4 | Chemie (PST) | |||
5 | A, B | PHOSPHATE ION | non-polymer | 95.0 | 3 | Chemie (PO4) | |||
6 | B, A | 1,2-ETHANEDIOL | non-polymer | 62.1 | 15 | Chemie (EDO) | |||
7 | B, A | MANGANESE (II) ION | non-polymer | 54.9 | 2 | Chemie (MN) | |||
8 | B, A | SULFATE ION | non-polymer | 96.1 | 4 | Chemie (SO4) | |||
9 | B, A | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) | |||
10 | 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 |
Sequence viewer
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 |