5GZ5
Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Snake venom phosphodiesterase (PDE) | polymer | 830 | 94728.8 | 1 | UniProt (by SIFTS) (A0A2D0TC04) | Naja atra | |
| 2 | B (B) | 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 | 748.7 | 1 | In PDB GlyTouCan (G81315DD) | |||
| 3 | C (C) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 1 | In PDB GlyTouCan (G21290RB) | |||
| 4 | D (D) | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 367.3 | 1 | In PDB GlyTouCan (G86851RC) | |||
| 5 | E, F, G (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 3 | Chemie (NAG) | |||
| 6 | H, I (A) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 7 | J (A) | CALCIUM ION | non-polymer | 40.1 | 1 | Chemie (CA) PubChem (271) | |||
| 8 | K (A) | ADENOSINE MONOPHOSPHATE | non-polymer | 347.2 | 1 | Chemie (AMP) PubChem (224) PubChem (34768) PubChem (83862) PubChem (446048) PubChem (515384) PubChem (638042) PubChem (5316444) PubChem (5742864) PubChem (12163610) PubChem (12358355) PubChem (16397049) PubChem (16760266) PubChem (40467049) PubChem (40469468) PubChem (44348067) PubChem (45358029) PubChem (46874558) PubChem (40459109) PubChem (46875232) PubChem (177678969) PubChem (6083) PubChem (1549371) PubChem (92144436) PubChem (57358045) PubChem (57879893) PubChem (57879902) PubChem (12358354) PubChem (122197642) PubChem (162290139) PubChem (162946266) PubChem (171699505) | |||
| 9 | L (A) | water | water | 18.0 | 804 | Chemie (HOH) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 1 |
| Total formula weight | 94728.8 | |
| Branched | Number of molecules | 3 |
| Total formula weight | 1686.6 | |
| Non-Polymers* | Number of molecules | 7 |
| Total formula weight | 1181.7 | |
| All* | Total formula weight | 97597.1 |
