MolNFT v1 · #54039 · protein + DNA
The 2.1A crystal structure of S. aureus gyrase complex with GSK299423 and DNA
2XCS · DNA gyrase subunit B, DNA gyrase subunit a: “The 2.1A crystal structure of S. aureus gyrase complex with GSK299423 and DNA”. X-ray diffraction, 2 ligands (RXV, MN), 16 pockets (best druggability 0.82). MolNFT v1 #54039 on GenesisL1…
- 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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