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5CDP

2.45A structure of etoposide with S.aureus DNA gyrase and DNA

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, C
(A, C)		DNA gyrase subunit Apolymer48354738.52UniProt (Q99XG5)Staphylococcus aureus (strain N315)
2B, D
(B, D)		DNA gyrase subunit Bpolymer19021345.32UniProt (P66937)Staphylococcus aureus (strain N315)Greek key deletion construct
3E, G
(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')polymer82451.62synthetic construct
4F, H
(G, H)		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')polymer133967.62synthetic construct
5I, N
(A, H)		SODIUM IONnon-polymer23.02Chemie (NA)
PubChem (923)
6J, K, L
(B, D, G)		MANGANESE (II) IONnon-polymer54.93Chemie (MN)
PubChem (27854)
7M
(H)		(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-glucopyranosidenon-polymer588.61Chemie (EVP)
PubChem (3310)
PubChem (439525)
PubChem (6604625)
PubChem (6610299)
PubChem (71163169)
PubChem (9851399)
PubChem (9916469)
PubChem (10077076)
PubChem (11072012)
PubChem (11758093)
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PubChem (11870445)
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8O, P, Q, R, S...
(A, B, C, D, E...)		waterwater18.0767Chemie (HOH)
Sequence modifications
A, C: 9 - 491 (UniProt: Q99XG5)
PDBExternal DatabaseDetails
Phe 123Tyr 123engineered mutation
B, D: 417 - 543 (UniProt: P66937)
B, D: 580 - 640 (UniProt: P66937)
PDBExternal DatabaseDetails
Thr 544-linker
Gly 545-linker
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains8
Total formula weight165005.9
Non-Polymers*Number of molecules6
Total formula weight799.4
All*Total formula weight165805.2
*Water molecules are not included.

251801

PDB entries from 2026-04-08

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