6QTK
2.31A structure of gepotidacin with S.aureus DNA gyrase and doubly nicked DNA
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | B, D | DNA gyrase subunit B | polymer | 202 | 22605.7 | 2 | UniProt (P66937) Pfam (PF01751) Pfam (PF00986) In PDB | Staphylococcus aureus (strain N315) | |
| 2 | A, C | DNA gyrase subunit A | polymer | 490 | 55521.3 | 2 | UniProt (Q99XG5) Pfam (PF00521) In PDB | Staphylococcus aureus | |
| 3 | E, F | DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | polymer | 20 | 6135.0 | 2 | synthetic construct | ||
| 4 | B, D | MANGANESE (II) ION | non-polymer | 54.9 | 2 | Chemie (MN) | |||
| 5 | A, C, E | GLYCEROL | non-polymer | 92.1 | 8 | Chemie (GOL) | |||
| 6 | A | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) | |||
| 7 | F | (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione | non-polymer | 448.5 | 1 | Chemie (JHN) | |||
| 8 | water | water | 18.0 | 823 | Chemie (HOH) |
Sequence modifications
B, D: 409 - 644 (UniProt: P66937)
A, C: 2 - 491 (UniProt: Q99XG5)
| PDB | External Database | Details |
|---|---|---|
| Met 409 | Leu 409 | conflict |
| - | 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 | conflict |
| Gly 545 | Arg 579 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Phe 123 | Tyr 123 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 168523.9 | |
| Non-Polymers* | Number of molecules | 12 |
| Total formula weight | 1318.1 | |
| All* | Total formula weight | 169842.1 |
