5CDO
3.15A structure of QPT-1 with S.aureus DNA gyrase and 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, G, I (A, C, R, T) | DNA gyrase subunit A | polymer | 482 | 54777.4 | 4 | UniProt (Q99XG5) Pfam (PF00521) | Staphylococcus aureus (strain N315) | |
| 2 | B, D, H, J (B, D, S, U) | DNA gyrase subunit B,DNA gyrase subunit B | polymer | 188 | 21111.0 | 4 | UniProt (P66937) Pfam (PF01751) Pfam (PF00986) | Staphylococcus aureus (strain N315) | |
| 3 | E, F, K, L (E, F, V, W) | DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | polymer | 20 | 6151.0 | 4 | synthetic construct | ||
| 4 | AA, BA, M (T, A) | SULFATE ION | non-polymer | 96.1 | 3 | Chemie (SO4) | |||
| 5 | CA, N, Q, R, X (T, A, C, R) | SODIUM ION | non-polymer | 23.0 | 5 | Chemie (NA) | |||
| 6 | EA, FA, O, T, U (U, A, D) | GLYCEROL | non-polymer | 92.1 | 5 | Chemie (GOL) | |||
| 7 | DA, P, S, Y (U, B, D, S) | MANGANESE (II) ION | non-polymer | 54.9 | 4 | Chemie (MN) | synthetic construct | ||
| 8 | GA, V (W, E) | (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one | non-polymer | 374.3 | 2 | Chemie (53M) | |||
| 9 | W (F) | (2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione | non-polymer | 374.3 | 1 | Chemie (53L) | |||
| 10 | Z (S) | (2R,4S,4aS,5R)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione | non-polymer | 374.3 | 1 | Chemie (50M) | |||
| 11 | HA, IA, JA, KA, LA... (A, B, C, D, E...) | water | water | 18.0 | 82 | Chemie (HOH) |
Sequence modifications
B, D, S, U: 417 - 638 (UniProt: P66937)
B, D, S, U: 580 - 638 (PDB: 5CDO)
| PDB | External Database | Details |
|---|---|---|
| - | Leu 544 | deletion |
| - | Tyr 545 | deletion |
| - | Lys 546 | deletion |
| - | Leu 547 | deletion |
| - | Thr 548 | deletion |
| - | Gln 549 | deletion |
| - | Gly 550 | deletion |
| - | Lys 551 | deletion |
| - | Gln 552 | deletion |
| - | Lys 553 | deletion |
| - | Tyr 554 | deletion |
| - | Tyr 555 | deletion |
| - | Val 556 | deletion |
| - | Tyr 557 | deletion |
| - | Asn 558 | deletion |
| - | Asp 559 | deletion |
| - | Arg 560 | deletion |
| - | Glu 561 | deletion |
| - | Leu 562 | deletion |
| - | Asp 563 | deletion |
| - | Lys 564 | deletion |
| - | Leu 565 | deletion |
| - | Lys 566 | deletion |
| - | Ser 567 | deletion |
| - | Glu 568 | deletion |
| - | Leu 569 | deletion |
| - | Asn 570 | deletion |
| - | Pro 571 | deletion |
| - | Thr 572 | deletion |
| - | Pro 573 | deletion |
| - | Lys 574 | deletion |
| - | Trp 575 | deletion |
| - | Ser 576 | deletion |
| - | Ile 577 | deletion |
| Thr 544 | Ala 578 | linker |
| Gly 545 | Arg 579 | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 328157.5 | |
| Non-Polymers* | Number of molecules | 21 |
| Total formula weight | 2580.8 | |
| All* | Total formula weight | 330738.2 |
