MolNFT v1 · #115904 · protein
Crystal structure of mycobacterium tuberculosis kstr in complex with peg
5CXG · Hth-type transcriptional repressor kstr: “Crystal structure of mycobacterium tuberculosis kstr in complex with peg”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #115904 on GenesisL1: 3D structure, binding sites…
- PDB
- 5CXG
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor kstr
- UniProt
- P96856
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor kstr | protein | 186 | 77% helix, 0% strand | P96856 |
| B | Hth-type transcriptional repressor kstr | protein | 184 | 79% helix, 0% strand | P96856 |
| C | Hth-type transcriptional repressor kstr | protein | 182 | 78% helix, 0% strand | P96856 |
| D | Hth-type transcriptional repressor kstr | protein | 176 | 78% helix, 0% strand | P96856 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.74 | 0.96 | 26 | empty |
| 2 | 129 | 0.73 | 0.92 | 25 | PGE |
| 3 | 141 | 0.68 | 0.88 | 26 | PGE |
| 4 | 508 | 0.59 | 0.74 | 52 | empty |
| 5 | 187 | 0.57 | 0.81 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1361 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1268 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CXG · Crystal structure of Mycobacterium tuberculosis KstR in complex with PEG · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.97
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 5CXG · PDBe 5CXG · UniProt P96856
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