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) PubChem (753) | |||
| 6 | N (A) | PENTAETHYLENE GLYCOL | non-polymer | 238.3 | 1 | Chemie (1PE) PubChem (62551) | |||
| 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) PubChem (312) | |||
| 9 | Y (A) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) PubChem (888) | |||
| 10 | CA, Z (C, E) | ADENOSINE MONOPHOSPHATE | non-polymer | 347.2 | 2 | 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) | |||
| 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 |
