Research workbench
Crystal structure of a rex-family transcriptional regulatory protein from streptococcus agalactiae complexed with NAD+
Analyse Crystal structure of a rex-family transcriptional regulatory protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEQ
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Redox-sensing transcriptional repressor rex
- UniProt
- Q8E565
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Redox-sensing transcriptional repressor rex | protein | 196 | 46% helix, 17% strand | Q8E565 |
| B | Redox-sensing transcriptional repressor rex | protein | 204 | 45% helix, 17% strand | Q8E565 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.80 | 0.81 | 69 | empty |
| 2 | 327 | 0.59 | 0.77 | 39 | empty |
| 3 | 260 | 0.59 | 0.79 | 37 | NAD |
| 4 | 56 | 0.34 | 0.77 | 14 | empty |
| 5 | 52 | 0.31 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 3037 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3KEQ · Crystal structure of a Rex-family transcriptional regulatory protein from Streptococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8E565 · AlphaFold monomer V2.0 prediction for redox-sensing transcriptional repressor rex (Q8E565) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q8E565
- Elsewhere: RCSB PDB 3KEQ · PDBe 3KEQ · UniProt Q8E565
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