8QMC
High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and 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 (ATP-hydrolyzing),DNA topoisomerase 4 subunit A | polymer | 742 | 84211.4 | 2 | UniProt (J0V1V8) UniProt (P72525) Pfam (PF00521) | Streptococcus pneumoniae | Topoisomerase IV subunit A |
| 2 | C (E) | DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3') | polymer | 7 | 2168.4 | 1 | DNA molecule | ||
| 3 | D (F) | DNA/RNA (5'-R(P*GP*G)-D(P*TP*T)-R(P*A)-D(P*T)-R(P*CP*CP*AP*CP*A)-3') | polymer | 11 | 3333.2 | 1 | DNA molecule | ||
| 4 | E (H) | DNA/RNA (5'-R(P*AP*AP*CP*CP*G)-D(P*T)-R(P*A)-D(P*TP*T)-R(P*AP*C)-3') | polymer | 11 | 3317.2 | 1 | DNA molecule | ||
| 5 | F (G) | DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3') | polymer | 7 | 2121.4 | 1 | DNA molecule | ||
| 6 | G, H (A) | MALONIC ACID | non-polymer | 104.1 | 2 | Chemie (MLA) | |||
| 7 | I, J (A) | ACETATE ION | non-polymer | 59.0 | 2 | Chemie (ACT) | |||
| 8 | K, L, M, P, Q... (A, B) | MAGNESIUM ION | non-polymer | 24.3 | 6 | Chemie (MG) | |||
| 9 | N, S (A, B) | CHLORIDE ION | non-polymer | 35.5 | 2 | Chemie (CL) | |||
| 10 | O (B) | (4S)-2-METHYL-2,4-PENTANEDIOL | non-polymer | 118.2 | 1 | Chemie (MPD) | |||
| 11 | T, U (F, H) | delafloxacin | non-polymer | 440.8 | 2 | Chemie (TE9) | |||
| 12 | AA, V, W, X, Y... (G, A, B, E, F...) | water | water | 18.0 | 426 | Chemie (HOH) |
Sequence modifications
A, B: 412 - 647 (UniProt: J0V1V8)
A, B: 1001 - 1488 (UniProt: P72525)
| PDB | External Database | Details |
|---|---|---|
| Met 403 | - | initiating methionine |
| Lys 404 | - | expression tag |
| Asn 405 | - | expression tag |
| Lys 406 | - | expression tag |
| Lys 407 | - | expression tag |
| Asp 408 | - | expression tag |
| Lys 409 | - | expression tag |
| Gly 410 | - | expression tag |
| Leu 411 | - | expression tag |
| His 648 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Thr 1257 | Ile 257 | conflict |
| 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 | 15 |
| Total formula weight | 1542.6 | |
| All* | Total formula weight | 180905.8 |
