Research workbench
DNA gyrase complexed with uncleaved DNA and compound 7 to 2.6A resolution
Analyse DNA gyrase complexed with uncleaved DNA and compound 7 to 2.6A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MVS
- Type
- protein + DNA
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit a; DNA (5'…
- EC
- 5.6.2.2
- UniProt
- P0A0K8, Q99XG5
- Ligands
- Y1W, MN, CL, SO4
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.6.2.2) | protein | 674 | 49% helix, 16% strand | P0A0K8, Q99XG5 |
| B | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.6.2.2) | protein | 675 | 48% helix, 16% strand | P0A0K8, Q99XG5 |
| C | DNA (5'- D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 20 | — | — |
| D | DNA (5'- D(P*AP*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
- Y1W · (1S)-2-[(2R,5S)-5-{[(2,3-dihydro-1,4-benzodioxin-6-yl) methyl]amino}-1,3-dioxan-2-yl]-1-(3-fluoro-6-methoxyquinolin-4-yl)ethan-1-ol · ligand · chains A, B, C, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.84 | 0.86 | 107 | Y1W |
| 2 | 495 | 0.73 | 0.82 | 32 | empty |
| 3 | 413 | 0.70 | 0.82 | 31 | empty |
| 4 | 389 | 0.65 | 0.79 | 49 | empty |
| 5 | 378 | 0.64 | 0.79 | 57 | CL |
Interfaces
6 interfaces between chains.
- A–B · 3112 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 983 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 968 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 920 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- B–C · 838 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 7MVS · DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution · the same entry in another collection · chain D against D, 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 0.71
- P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain B 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 P0A0K8
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 7MVS · PDBe 7MVS · UniProt P0A0K8 · UniProt Q99XG5
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