MolNFT v1 · #54040 · protein + DNA
The twinned 3.35A structure of S. aureus gyrase complex with ciprofloxacin and DNA
2XCT · DNA gyrase subunit B, DNA gyrase subunit a: “The twinned 3.35A structure of S. aureus gyrase complex with ciprofloxacin and DNA”. X-ray diffraction, 2 ligands (CPF, MN), 20 pockets (best druggability 0.82). MolNFT v1 #54040 on…
- 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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