Research workbench
2.45A structure of etoposide with S.AUREUS DNA gyrase and DNA
Analyse 2.45A 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
- 5CDP
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- Q99XG5, P66937
- Ligands
- EVP, MN, NA
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 483 | 48% helix, 18% strand | Q99XG5 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 190 | 47% helix, 13% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 18% strand | Q99XG5 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 47% helix, 12% strand | P66937 |
| 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') | dna | 8 | — | — |
| G | 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') | dna | 12 | — | — |
| 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') | dna | 11 | — | — |
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 · chains A, B, C, E, G, H
- MN · Manganese (II) ion · metal · 3 copies · chains B, D, F, A, G
- NA · Sodium ion · metal · 2 copies · chains A, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.84 | 0.85 | 105 | MN, EVP, NA |
| 2 | 296 | 0.75 | 0.87 | 45 | empty |
| 3 | 430 | 0.74 | 0.84 | 31 | empty |
| 4 | 410 | 0.70 | 0.82 | 33 | empty |
| 5 | 50 | 0.68 | 0.97 | 24 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1750 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1457 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 648 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5CDP · 2.45A structure of etoposide with S.aureus DNA gyrase and DNA · the same entry in another collection · chain H against H, TM-score 1.00
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5CDP · PDBe 5CDP · UniProt Q99XG5 · UniProt P66937
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