MolNFT v1 · #119127 · protein + DNA
Kstr, transcriptional repressor of cholesterol degradation in mycobacterium tuberculosis, bound to the DNA operator
5FMP · Hth-type transcriptional repressor kstr: “Kstr, transcriptional repressor of cholesterol degradation in mycobacterium tuberculosis, bound to the DNA…”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #119127 on…
- PDB
- 5FMP
- Type
- protein + DNA
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor kstr; 5'-D(*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*A…
- UniProt
- P96856
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor kstr | protein | 184 | 80% helix, 0% strand | P96856 |
| B | Hth-type transcriptional repressor kstr | protein | 183 | 83% helix, 0% strand | P96856 |
| C | 5'-D(*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*A)-3' | dna | 16 | — | — |
| D | 5'-D(*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*G)-3' | dna | 16 | — | — |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.68 | 0.76 | 49 | empty |
| 2 | 162 | 0.67 | 0.87 | 47 | empty |
| 3 | 93 | 0.65 | 0.90 | 32 | empty |
| 4 | 61 | 0.50 | 0.86 | 19 | empty |
| 5 | 56 | 0.33 | 0.78 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1425 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 713 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–D · 373 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 367 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 257 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 5FMP · KstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis… · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.95
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 5FMP · PDBe 5FMP · UniProt P96856
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