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Crystal structure of moxifloxacin, DNA, and a. baumannii topo IV (pare-parc fusion truncate)
Analyse Crystal structure of moxifloxacin, DNA, and a. baumannii topo IV (pare-parc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKK
- Type
- protein + DNA
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase IV; DNA
- EC
- 5.99.1.-
- UniProt
- B0V9T6, B0VP98
- Ligands
- MFX, MG
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Topoisomerase IV (EC 5.99.1.-) | protein | 692 | 47% helix, 15% strand | B0V9T6, B0VP98 |
| C | Topoisomerase IV (EC 5.99.1.-) | protein | 711 | 46% helix, 15% strand | B0V9T6, B0VP98 |
| E | DNA | dna | 26 | — | — |
| F | DNA | dna | 26 | — | — |
Ligands and binding sites
- MFX · 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 2 copies · chains A, C, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.85 | 0.88 | 108 | MG, MFX |
| 2 | 439 | 0.79 | 0.87 | 45 | MFX |
| 3 | 297 | 0.76 | 0.89 | 31 | empty |
| 4 | 648 | 0.74 | 0.80 | 84 | empty |
| 5 | 475 | 0.66 | 0.78 | 61 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2729 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1100 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–F · 1060 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–E · 982 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–E · 869 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2XKK · CRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, and A. BAUMANNII TOPO IV (PARE-PARC FUSION… · the same entry in another collection · chain A against A, 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 B0V9T6
- Every structure of UniProt B0VP98
- Elsewhere: RCSB PDB 2XKK · PDBe 2XKK · UniProt B0V9T6 · UniProt B0VP98
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