MolNFT v1 · #67451 · protein + DNA
Crystal structure of a rex-family REPRESSOR/DNA/NAD+ complex from thermus aquaticus
3IKT · Redox-sensing transcriptional repressor rex: “Crystal structure of a rex-family REPRESSOR/DNA/NAD+ complex from thermus aquaticus”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.78). MolNFT v1 #67451 on…
- PDB
- 3IKT
- Type
- protein + DNA
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Redox-sensing transcriptional repressor rex; Rex operator DNA
- UniProt
- Q72I39
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Redox-sensing transcriptional repressor rex | protein | 204 | 43% helix, 18% strand | Q72I39 |
| B | Redox-sensing transcriptional repressor rex | protein | 206 | 41% helix, 18% strand | Q72I39 |
| C, D | Rex operator DNA | dna | 22 | — | — |
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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.78 | 0.80 | 99 | NAD |
| 2 | 970 | 0.75 | 0.78 | 94 | empty |
| 3 | 99 | 0.36 | 0.74 | 13 | empty |
| 4 | 69 | 0.35 | 0.77 | 12 | empty |
| 5 | 55 | 0.29 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2682 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1041 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- B–D · 519 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 504 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 436 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3IKT · Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus · the same entry in another collection · chain A against A, TM-score 1.00
- Q72I39 · AlphaFold monomer V2.0 prediction for redox-sensing transcriptional repressor rex (Q72I39) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q72I39
- Elsewhere: RCSB PDB 3IKT · PDBe 3IKT · UniProt Q72I39
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