6DT1
Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate
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, E) | DNA ligase | polymer | 507 | 57540.9 | 2 | UniProt (P00970) Pfam (PF01068) | Enterobacteria phage T4 (Bacteriophage T4) | Polydeoxyribonucleotide synthase [ATP] |
| 2 | C, F (B, F) | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3') | polymer | 11 | 3349.2 | 2 | Enterobacteria phage T4 | ||
| 3 | D, G (C, G) | DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3') | polymer | 10 | 3085.0 | 2 | Enterobacteria phage T4 | ||
| 4 | E, H (D, H) | DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | polymer | 21 | 6393.1 | 2 | Enterobacteria phage T4 | ||
| 5 | I, J, K, L, M... (A) | GLYCEROL | non-polymer | 92.1 | 12 | Chemie (GOL) | |||
| 6 | N (A) | PENTAETHYLENE GLYCOL | non-polymer | 238.3 | 1 | Chemie (1PE) | |||
| 7 | BA, DA, EA, T, U (B, D, A) | 2,3-DIHYDROXY-1,4-DITHIOBUTANE | non-polymer | 154.3 | 5 | Chemie (DTT) | |||
| 8 | AA, X (E, A) | CHLORIDE ION | non-polymer | 35.5 | 2 | Chemie (CL) | |||
| 9 | Y (A) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 10 | CA, Z (C, E) | ADENOSINE MONOPHOSPHATE | non-polymer | 347.2 | 2 | Chemie (AMP) | |||
| 11 | FA, GA, HA, IA, JA... (A, E, B, C, D...) | water | water | 18.0 | 267 | Chemie (HOH) |
Sequence modifications
A, E: 1 - 487 (UniProt: P00970)
| PDB | External Database | Details |
|---|---|---|
| Met -19 | - | initiating methionine |
| Gly -18 | - | expression tag |
| Ser -17 | - | expression tag |
| Ser -16 | - | expression tag |
| His -15 | - | expression tag |
| His -14 | - | expression tag |
| His -13 | - | expression tag |
| His -12 | - | expression tag |
| His -11 | - | expression tag |
| His -10 | - | expression tag |
| Ser -9 | - | expression tag |
| Ser -8 | - | expression tag |
| Gly -7 | - | expression tag |
| Leu -6 | - | expression tag |
| Val -5 | - | expression tag |
| Pro -4 | - | expression tag |
| Arg -3 | - | expression tag |
| Gly -2 | - | expression tag |
| Ser -1 | - | expression tag |
| His 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 8 |
| Total formula weight | 140736.5 | |
| Non-Polymers* | Number of molecules | 23 |
| Total formula weight | 2904.3 | |
| All* | Total formula weight | 143640.8 |
