5CDN
2.8A structure of etoposide 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, I, K (A, C, R, T) | DNA gyrase subunit A | polymer | 481 | 54664.2 | 4 | UniProt (Q99XG5) | Staphylococcus aureus | |
| 2 | B, D, J, L (B, D, S, U) | DNA gyrase subunit B,DNA gyrase subunit B | polymer | 189 | 21274.2 | 4 | UniProt (P66937) | Staphylococcus aureus (strain N315) | |
| 3 | E, G, M, O (E, F, V, W) | DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3') | polymer | 8 | 2451.6 | 4 | synthetic construct | ||
| 4 | F, H, N, P (G, O, N, P) | DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3') | polymer | 12 | 3639.4 | 4 | synthetic construct | ||
| 5 | Q (A) | SULFATE ION | non-polymer | 96.1 | 1 | Chemie (SO4) | |||
| 6 | BA, R, V, Z (U, B, D, S) | MANGANESE (II) ION | non-polymer | 54.9 | 4 | Chemie (MN) PubChem (27854) | |||
| 7 | AA, S, U, W (T, C, E) | GLYCEROL | non-polymer | 92.1 | 4 | Chemie (GOL) PubChem (753) | |||
| 8 | T (C) | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) PubChem (923) | |||
| 9 | CA, DA, X, Y (N, P, G, O) | (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside | non-polymer | 588.6 | 4 | Chemie (EVP) PubChem (16394664) PubChem (16401497) PubChem (17571827) PubChem (3310) PubChem (24214025) PubChem (16757762) PubChem (439525) PubChem (44291969) PubChem (44343101) PubChem (44439411) PubChem (23947062) PubChem (45356822) PubChem (40469452) PubChem (44399307) PubChem (50989217) PubChem (50936917) PubChem (57835439) PubChem (58934286) PubChem (54395107) PubChem (59516320) PubChem (59890041) PubChem (59935043) PubChem (59969579) PubChem (59981749) PubChem (59981750) PubChem (60046278) PubChem (56841827) PubChem (59360017) PubChem (68028947) PubChem (59910346) PubChem (59991120) PubChem (70840214) PubChem (70973405) PubChem (68297502) PubChem (143627016) PubChem (143179527) PubChem (71774979) PubChem (73707413) PubChem (36462) PubChem (6604625) PubChem (6610299) PubChem (284997) PubChem (90657341) PubChem (90721503) PubChem (90928389) PubChem (71163169) PubChem (9851399) PubChem (73896870) PubChem (9916469) PubChem (487698) PubChem (10077076) PubChem (92209272) PubChem (92209274) PubChem (92209275) PubChem (92215927) PubChem (92481364) PubChem (11072012) PubChem (11758093) PubChem (89809018) PubChem (11870245) PubChem (11870445) PubChem (96545492) PubChem (13269634) PubChem (13269638) PubChem (91528489) PubChem (98044670) PubChem (98047570) PubChem (98047571) PubChem (98047572) PubChem (98456096) PubChem (98456098) PubChem (92209273) PubChem (71109688) PubChem (92211248) PubChem (92481363) PubChem (5284558) PubChem (99940884) PubChem (101060364) PubChem (98044669) PubChem (98456097) PubChem (99940883) PubChem (100810256) PubChem (6419930) PubChem (101616479) PubChem (101872048) PubChem (6604389) PubChem (122535989) PubChem (6708815) PubChem (124747955) PubChem (9851398) PubChem (129010358) PubChem (129427216) PubChem (129426541) PubChem (129539581) PubChem (129427217) PubChem (129539582) PubChem (117627571) PubChem (117987058) PubChem (134694737) PubChem (11870443) PubChem (11870444) PubChem (124747952) PubChem (124747953) PubChem (124747954) PubChem (124762382) PubChem (137370657) PubChem (129406641) PubChem (129416190) PubChem (129426542) PubChem (129426543) PubChem (129539580) PubChem (129539583) PubChem (13269642) PubChem (142236013) PubChem (146156165) PubChem (155239770) PubChem (135056244) PubChem (137704929) PubChem (144658263) PubChem (145365700) PubChem (153427708) PubChem (171042228) PubChem (154700020) PubChem (156133909) PubChem (172012121) PubChem (163016457) PubChem (163016458) PubChem (163016459) PubChem (163016460) PubChem (163016461) PubChem (164643737) PubChem (164935527) PubChem (167092395) PubChem (168251311) PubChem (169440327) PubChem (172372122) | |||
| 10 | EA, FA, GA, HA, IA... (A, B, C, D, E...) | water | water | 18.0 | 412 | Chemie (HOH) |
Sequence modifications
B, D, S, U: 417 - 543 (UniProt: P66937)
B, D, S, U: 580 - 639 (UniProt: P66937)
B, D, S, U: 580 - 639 (UniProt: P66937)
| PDB | External Database | Details |
|---|---|---|
| Thr 544 | - | linker |
| Gly 545 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 16 |
| Total formula weight | 328117.6 | |
| Non-Polymers* | Number of molecules | 14 |
| Total formula weight | 3061.4 | |
| All* | Total formula weight | 331179.1 |
