Research workbench
The 3.1A crystal structure of the catalytic core (B'A' region) of staphylococcus aureus DNA gyrase
Analyse The 3.1A crystal structure of the catalytic core (B'A' region) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCO
- Type
- protein
- Length
- 636 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B, DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- CA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 636 | 45% helix, 16% strand | P66937, Q99XG5 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.61 | 0.79 | 49 | empty |
| 2 | 212 | 0.47 | 0.74 | 32 | empty |
| 3 | 125 | 0.46 | 0.78 | 22 | empty |
| 4 | 104 | 0.35 | 0.73 | 25 | empty |
| 5 | 59 | 0.33 | 0.76 | 11 | empty |
Compared structures
- 2XCO · The 3.1A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.72
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain A against A, TM-score 0.24
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 2XCO · PDBe 2XCO · UniProt P66937 · UniProt Q99XG5
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