9IX4
Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C (A, B) | DdmD | polymer | 1192 | 137294.7 | 2 | UniProt (A0A5R8LS59) | Lacticaseibacillus | |
| 2 | B (C) | DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3') | polymer | 13 | 3965.6 | 1 | Lacticaseibacillus | ||
| 3 | D (D) | DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3') | polymer | 12 | 3661.4 | 1 | Lacticaseibacillus | ||
| 4 | E, F (E, F) | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | polymer | 10 | 3087.1 | 2 | Lacticaseibacillus | ||
| 5 | G, H (A, B) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 2 | Chemie (ADP) |
Sequence modifications
A, B: 1 - 1192 (UniProt: A0A5R8LS59)
| PDB | External Database | Details |
|---|---|---|
| Ser 7 | Leu 7 | conflict |
| Ile 46 | Val 46 | conflict |
| Ser 115 | Asn 115 | conflict |
| Glu 154 | Asp 154 | conflict |
| Lys 174 | Arg 174 | conflict |
| Ala 179 | Glu 179 | conflict |
| Asp 187 | Asn 187 | conflict |
| Phe 313 | Ser 313 | conflict |
| His 468 | Tyr 468 | conflict |
| Glu 575 | Gln 575 | conflict |
| Asp 681 | Glu 681 | conflict |
| Ile 704 | Val 704 | conflict |
| Arg 762 | Pro 762 | conflict |
| Pro 859 | Thr 859 | conflict |
| Val 1090 | Ala 1090 | conflict |
| Asp 1101 | Asn 1101 | conflict |
| Ala 1106 | Val 1106 | conflict |
| Arg 1140 | Gln 1140 | conflict |
| Thr 1165 | Met 1165 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 288390.7 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 854.4 | |
| All* | Total formula weight | 289245.1 |
