Research workbench
Mycobacterium tuberculosis kstr in complex with a 18-bp DNA operator
Analyse Mycobacterium tuberculosis kstr in complex with a 18-bp DNA operator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UA1
- Type
- protein + DNA
- Length
- 427 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor kstr; DNA (5'…
- UniProt
- P96856
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hth-type transcriptional repressor kstr | protein | 178 | 80% helix, 0% strand | P96856 |
| A | Hth-type transcriptional repressor kstr | protein | 177 | 80% helix, 0% strand | P96856 |
| C, E | DNA (5'- D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3') | dna | 18 | — | — |
| D, F | DNA (5'- D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, A, C, E, F
- PGE · Triethylene glycol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.75 | 0.85 | 36 | empty |
| 2 | 290 | 0.72 | 0.85 | 36 | empty |
| 3 | 652 | 0.69 | 0.78 | 52 | empty |
| 4 | 92 | 0.50 | 0.82 | 21 | empty |
| 5 | 74 | 0.49 | 0.84 | 21 | empty |
Interfaces
15 interfaces between chains.
- D–E · 2055 Ų buried · 720 hydrogen bonds · nucleic-nucleic
- C–F · 2054 Ų buried · 733 hydrogen bonds · nucleic-nucleic
- B–A · 1418 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 789 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- C–D · 784 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Compared structures
- 5UA1 · Mycobacterium tuberculosis KstR in complex with a 18-bp DNA operator · the same entry in another collection · chain F against F, TM-score 1.00
- P96856 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor kstr (P96856) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P96856
- Elsewhere: RCSB PDB 5UA1 · PDBe 5UA1 · UniProt P96856
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