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The 3.5A crystal structure of the catalytic core (B'A' region) of staphylococcus aureus DNA gyrase complexed with GSK299423 and DNA
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- PDB
- 2XCR
- Type
- protein + DNA
- Length
- 2,948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B, DNA gyrase subunit a; 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- 5UA, RXV
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 718 | 40% helix, 14% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 719 | 41% helix, 15% strand | P66937, Q99XG5 |
| E, F | 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3' | dna | 19 | — | — |
| S | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 718 | 43% helix, 14% strand | P66937, Q99XG5 |
| U | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 717 | 41% helix, 15% strand | P66937, Q99XG5 |
| V | 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3' | dna | 20 | — | — |
| W | 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3' | dna | 18 | — | — |
Ligands and binding sites
- 5UA · 5'-O-carboxy-2'-deoxyadenosine · ligand · 2 copies · chains E, F, D
- RXV · 6-methoxy-4-(2-{4-[([1,3]oxathiolo[5,4-c]pyridin-6-ylmethyl)amino]piperidin-1-yl}ethyl)quinoline-3-carbonitrile · ligand · 2 copies · chains B, D, E, F, S, U, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.86 | 0.88 | 105 | empty |
| 2 | 545 | 0.82 | 0.88 | 61 | empty |
| 3 | 685 | 0.79 | 0.84 | 70 | RXV |
| 4 | 1115 | 0.76 | 0.78 | 92 | empty |
| 5 | 267 | 0.76 | 0.89 | 25 | empty |
Interfaces
13 interfaces between chains.
- S–U · 3299 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 3267 Ų buried · 39 hydrogen bonds · protein-protein
- B–U · 1430 Ų buried · 16 hydrogen bonds · protein-protein
- S–V · 997 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–F · 964 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 2XCR · The 3.5A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus… · the same entry in another collection · chain W against W, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain D against A, TM-score 0.67
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 2XCR · PDBe 2XCR · UniProt P66937 · UniProt Q99XG5
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