Research workbench
2.8A structure of etoposide with S.AUREUS DNA gyrase and DNA
Analyse 2.8A structure of etoposide with S.AUREUS DNA gyrase and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CDN
- Type
- protein + DNA
- Length
- 2,748 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B,DNA gyrase subunit B; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- Q99XG5, P66937
- Ligands
- EVP, MN, NA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, T | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 50% helix, 17% strand | Q99XG5 |
| B, S | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 188 | 45% helix, 13% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 480 | 51% helix, 17% strand | Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 187 | 48% helix, 13% strand | P66937 |
| 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') | dna | 8 | — | — |
| G, 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') | dna | 12 | — | — |
| O | 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') | dna | 11 | — | — |
| R | DNA gyrase subunit a (EC 5.99.1.3) | protein | 475 | 50% helix, 17% strand | Q99XG5 |
| U | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 48% helix, 13% strand | P66937 |
Ligands and binding sites
- EVP · (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 · ligand · 4 copies · chains A, B, C, G, F, O, D, E, R, S, T, N, W, P, U, V
- MN · Manganese (II) ion · metal · 4 copies · chains B, D, S, U
- NA · Sodium ion · metal · chains C
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains C, E, O, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.83 | 0.85 | 92 | GOL, MN, EVP |
| 2 | 563 | 0.81 | 0.87 | 83 | MN, EVP |
| 3 | 495 | 0.79 | 0.86 | 35 | empty |
| 4 | 348 | 0.78 | 0.89 | 27 | empty |
| 5 | 513 | 0.76 | 0.84 | 39 | empty |
Interfaces
42 interfaces between chains.
- A–C · 1695 Ų buried · 30 hydrogen bonds · protein-protein
- R–T · 1660 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1434 Ų buried · 14 hydrogen bonds · protein-protein
- R–S · 1389 Ų buried · 15 hydrogen bonds · protein-protein
- T–U · 1337 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5CDN · 2.8A structure of etoposide with S.aureus DNA gyrase and DNA · the same entry in another collection · chain P against P, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q99XG5
- Every structure of UniProt P66937
- Elsewhere: RCSB PDB 5CDN · PDBe 5CDN · UniProt Q99XG5 · UniProt P66937
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