Research workbench
Crystal structure of the first part of the mycobacterium tuberculosis DNA gyrase reaction core: the breakage and reunion domain at 2.7 a resolution
Analyse Crystal structure of the first part of the mycobacterium tuberculosis DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IFZ
- Type
- protein
- Length
- 960 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- Q07702
- Ligands
- NA
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 487 | 50% helix, 15% strand | Q07702 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 473 | 49% helix, 17% strand | Q07702 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.63 | 0.78 | 51 | MPD |
| 2 | 123 | 0.63 | 0.87 | 25 | MPD |
| 3 | 165 | 0.48 | 0.77 | 22 | empty |
| 4 | 140 | 0.44 | 0.76 | 21 | empty |
| 5 | 155 | 0.43 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2016 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3IFZ · crystal structure of the first part of the Mycobacterium tuberculosis DNA gyrase reaction… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q07702
- Elsewhere: RCSB PDB 3IFZ · PDBe 3IFZ · UniProt Q07702
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