Research workbench
2.95A structure of moxifloxacin with S.AUREUS DNA gyrase and DNA
Analyse 2.95A structure of moxifloxacin 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
- 5CDQ
- Type
- protein + DNA
- Length
- 2,767 residues
- Chains
- 12
- 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
- MFX, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, R, T | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 17% strand | Q99XG5 |
| B | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 191 | 48% helix, 14% strand | P66937 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 190 | 43% helix, 12% strand | P66937 |
| E, F, V | DNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 19 | — | — |
| S | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 193 | 44% helix, 14% strand | P66937 |
| U | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 192 | 44% helix, 14% strand | P66937 |
| W | DNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 20 | — | — |
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 · 6 copies · chains A, B, C, E, F, D, R, S, T, V, W, U
- MG · Magnesium ion · metal · 14 copies · chains A, E, F, B, C, D, R, W, S, T, V, U
- GOL · Glycerol · additive · 8 copies · chains A, C, R, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.86 | 0.88 | 124 | MG, MFX |
| 2 | 325 | 0.75 | 0.87 | 44 | MFX |
| 3 | 237 | 0.73 | 0.88 | 41 | MFX |
| 4 | 211 | 0.72 | 0.89 | 37 | MG, MFX |
| 5 | 204 | 0.72 | 0.89 | 45 | empty |
Interfaces
30 interfaces between chains.
- A–C · 1875 Ų buried · 27 hydrogen bonds · protein-protein
- R–T · 1858 Ų buried · 25 hydrogen bonds · protein-protein
- R–S · 1490 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1450 Ų buried · 16 hydrogen bonds · protein-protein
- T–U · 1358 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 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 0.99
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain B 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 5CDQ · PDBe 5CDQ · UniProt Q99XG5 · UniProt P66937
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