4MDZ
Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre
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) | Metal dependent phosphohydrolase | polymer | 369 | 42765.8 | 2 | UniProt (C0QQ26) Pfam (PF01590) Pfam (PF13487) | Persephonella marina | |
| 2 | C, D, E, K (A, B) | FE (III) ION | non-polymer | 55.8 | 4 | Chemie (FE) | |||
| 3 | F, G, H, I, J (A) | SUCCINIC ACID | non-polymer | 118.1 | 5 | Chemie (SIN) | |||
| 4 | L (B) | 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) | non-polymer | 690.4 | 1 | Chemie (C2E) | |||
| 5 | M, N (A, B) | water | water | 18.0 | 96 | Chemie (HOH) |
Sequence modifications
A, B: 2 - 363 (UniProt: C0QQ26)
| PDB | External Database | Details |
|---|---|---|
| Gly -5 | - | expression tag |
| Pro -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Tyr -2 | - | expression tag |
| Gln -1 | - | expression tag |
| Asp 0 | - | expression tag |
| Pro 1 | - | expression tag |
| Ala 41 | Cys 41 | engineered mutation |
| Ala 197 | Cys 197 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 85531.6 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 1504.2 | |
| All* | Total formula weight | 87035.8 |
