8QMB
Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin
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) | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A | polymer | 742 | 84211.4 | 2 | UniProt (Q59961) UniProt (P72525) Pfam (PF01751) Pfam (PF00986) Pfam (PF00521) | Streptococcus pneumoniae | Topoisomerase IV subunit B,Topoisomerase IV subunit A |
| 2 | C (E) | DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3') | polymer | 7 | 2168.4 | 1 | Escherichia coli | ||
| 3 | D (F) | DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3') | polymer | 11 | 3333.2 | 1 | Escherichia coli | ||
| 4 | E (G) | DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3') | polymer | 7 | 2121.4 | 1 | Escherichia coli | ||
| 5 | F (H) | DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3') | polymer | 11 | 3317.2 | 1 | Escherichia coli | ||
| 6 | G, H, I, S, T... (A, B) | MAGNESIUM ION | non-polymer | 24.3 | 6 | Chemie (MG) | |||
| 7 | J, V (A, B) | CHLORIDE ION | non-polymer | 35.5 | 2 | Chemie (CL) | |||
| 8 | K, L, Z (A, B) | (4S)-2-METHYL-2,4-PENTANEDIOL | non-polymer | 118.2 | 3 | Chemie (MPD) | |||
| 9 | M, O (A) | MALONIC ACID | non-polymer | 104.1 | 2 | Chemie (MLA) | |||
| 10 | N, Q, W, X (A, B) | ACETATE ION | non-polymer | 59.0 | 4 | Chemie (ACT) | |||
| 11 | AA, P, R, Y (B, A) | FORMIC ACID | non-polymer | 46.0 | 4 | Chemie (FMT) | |||
| 12 | BA, CA (F, H) | delafloxacin | non-polymer | 440.8 | 2 | Chemie (TE9) | |||
| 13 | DA, EA, FA, GA, HA... (A, B, E, F, G...) | water | water | 18.0 | 1059 | Chemie (HOH) |
Sequence modifications
A, B: 404 - 647 (UniProt: Q59961)
A, B: 1001 - 1488 (UniProt: P72525)
| PDB | External Database | Details |
|---|---|---|
| Met 403 | - | initiating methionine |
| Ile 460 | Val 460 | variant |
| Ala 644 | Thr 644 | variant |
| His 648 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Thr 1257 | Ile 257 | variant |
| Leu 1489 | - | expression tag |
| Glu 1490 | - | expression tag |
| His 1491 | - | expression tag |
| His 1492 | - | expression tag |
| His 1493 | - | expression tag |
| His 1494 | - | expression tag |
| His 1495 | - | expression tag |
| His 1496 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 179363.1 | |
| Non-Polymers* | Number of molecules | 23 |
| Total formula weight | 2081.2 | |
| All* | Total formula weight | 181444.3 |
