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The 2.1A crystal structure of S. aureus gyrase complex with GSK299423 and DNA
Analyse The 2.1A crystal structure of S. aureus gyrase complex with GSK299423 and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCS
- Type
- protein + DNA
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B, DNA gyrase subunit a; 5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- RXV, MN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 672 | 48% helix, 16% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 670 | 48% helix, 16% strand | P66937, Q99XG5 |
| E | 5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP *CP*TP*AP*CP*GP*GP*CP*T)-3' | dna | 20 | — | — |
| F | 5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP *CP*TP*AP*CP*GP*GP*CP*T)-3' | dna | 19 | — | — |
Ligands and binding sites
- RXV · 6-methoxy-4-(2-{4-[([1,3]oxathiolo[5,4-c]pyridin-6-ylmethyl)amino]piperidin-1-yl}ethyl)quinoline-3-carbonitrile · ligand · chains B, D, E, F
- MN · Manganese (II) ion · metal · 4 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.82 | 0.84 | 97 | RXV |
| 2 | 482 | 0.74 | 0.83 | 33 | empty |
| 3 | 395 | 0.68 | 0.81 | 30 | empty |
| 4 | 393 | 0.64 | 0.79 | 49 | empty |
| 5 | 472 | 0.63 | 0.76 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3075 Ų buried · 44 hydrogen bonds · protein-protein
- D–F · 989 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–E · 980 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–F · 923 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- D–E · 834 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2XCS · The 2.1A crystal structure of S. aureus Gyrase complex with GSK299423 and DNA · the same entry in another collection · chain F against F, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain B against A, TM-score 0.71
- 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 0.28
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 2XCS · PDBe 2XCS · UniProt P66937 · UniProt Q99XG5
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