MolNFT v1 · #162049 · protein + DNA
2.7A structure of benzoisoxazole 3 with S.AUREUS DNA gyrase and DNA.
6QX1 · DNA gyrase subunit B: “2.7A structure of benzoisoxazole 3 with S.AUREUS DNA gyrase and DNA.”. X-ray diffraction, 4 ligands (JK8, GLY, MN), 16 pockets (best druggability 0.83). MolNFT v1 #162049 on GenesisL1: 3D structure, binding…
- PDB
- 6QX1
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B; DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- JK8, GLY, MN, CL
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 47% helix, 13% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 483 | 49% helix, 18% strand | Q99XG5 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 18% strand | Q99XG5 |
| E, F | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 20 | — | — |
Ligands and binding sites
- JK8 · (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine · ligand · 2 copies · chains B, A, D, C
- GLY · Glycine · ligand · chains C
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 5 copies · chains A, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.85 | 103 | GOL |
| 2 | 476 | 0.74 | 0.83 | 36 | empty |
| 3 | 449 | 0.71 | 0.81 | 32 | empty |
| 4 | 421 | 0.69 | 0.81 | 66 | MN, GOL |
| 5 | 379 | 0.68 | 0.81 | 58 | MN |
Interfaces
14 interfaces between chains.
- A–C · 1715 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 1452 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1427 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 987 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- B–C · 681 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QX1 · 2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA. · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.99
- 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 0.98
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 P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 6QX1 · PDBe 6QX1 · UniProt P66937 · UniProt Q99XG5
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