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The twinned 3.35A structure of S. aureus gyrase complex with ciprofloxacin and DNA
Analyse The twinned 3.35A structure of S. aureus gyrase complex with ciprofloxacin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCT
- Type
- protein + DNA
- Length
- 2,741 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B, DNA gyrase subunit a; 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- CPF, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 669 | 47% helix, 15% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 669 | 46% helix, 15% strand | P66937, Q99XG5 |
| E, V | 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' | dna | 7 | — | — |
| F | 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' | dna | 7 | — | — |
| G, X | 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' | dna | 11 | — | — |
| H | 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' | dna | 12 | — | — |
| S | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 666 | 43% helix, 12% strand | P66937, Q99XG5 |
| U | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 665 | 46% helix, 12% strand | P66937, Q99XG5 |
| W | 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' | dna | 6 | — | — |
| Y | 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' | dna | 11 | — | — |
Ligands and binding sites
- CPF · 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic acid · ligand · 4 copies · chains B, E, G, H, D, F, S, U, W, X, Y, V
- MN · Manganese (II) ion · metal · 8 copies · chains B, D, F, H, G, S, W, U, V, Y, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.82 | 0.83 | 101 | MN, CPF |
| 2 | 1129 | 0.80 | 0.82 | 116 | MN, CPF |
| 3 | 515 | 0.78 | 0.86 | 57 | MN |
| 4 | 628 | 0.78 | 0.84 | 46 | empty |
| 5 | 378 | 0.75 | 0.86 | 41 | empty |
Interfaces
26 interfaces between chains.
- S–U · 4124 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2331 Ų buried · 26 hydrogen bonds · protein-protein
- D–G · 835 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 767 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–H · 762 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 2XCT · The twinned 3.35A structure of S. aureus Gyrase complex with Ciprofloxacin and DNA · the same entry in another collection · chain Y against Y, 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 P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 2XCT · PDBe 2XCT · UniProt P66937 · UniProt Q99XG5
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