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Structure of bacillus subtilis hxlr, wild type in complex with formaldehyde and DNA
Analyse Structure of bacillus subtilis hxlr, wild type in complex with formaldehyde and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BZG
- Type
- protein + DNA
- Length
- 780 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional activator hxlr; DNA (5'…
- UniProt
- P42406
- Ligands
- MG, FOR
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, I, J | Hth-type transcriptional activator hxlr | protein | 110 | 60% helix, 13% strand | P42406 |
| C, D, G, H, K, L | DNA (5'- D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains B, C, F, G, H, K, L
- FOR · Formyl group · ion · 6 copies · chains A, B, E, F, I, J
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, E, F, J
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A, C, D, I, K, L
- PEG · Di(hydroxyethyl)ether · additive · chains E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1059 | 0.72 | 0.76 | 44 | empty |
| 2 | 1100 | 0.72 | 0.76 | 60 | empty |
| 3 | 1076 | 0.71 | 0.76 | 48 | empty |
| 4 | 452 | 0.58 | 0.74 | 30 | MG |
| 5 | 55 | 0.27 | 0.74 | 13 | empty |
Interfaces
22 interfaces between chains.
- E–F · 1785 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1783 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1738 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 919 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- G–H · 902 Ų buried · 77 hydrogen bonds · nucleic-nucleic
Compared structures
- 7BZG · Structure of Bacillus subtilis HxlR, wild type in complex with formaldehyde and DNA · the same entry in another collection · chain L against L, 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 P42406
- Elsewhere: RCSB PDB 7BZG · PDBe 7BZG · UniProt P42406
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