MolNFT v1 · #124195 · protein + DNA
Crystal structure of aibr in complex with isovaleryl coenzyme a and operator DNA
5K7Z · Transcriptional regulator, tetr family: “Crystal structure of aibr in complex with isovaleryl coenzyme a and operator DNA”. X-ray diffraction, 1 ligand (IVC), 8 pockets (best druggability 0.80). MolNFT v1 #124195 on GenesisL1: 3D…
- PDB
- 5K7Z
- Type
- protein + DNA
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, tetr family; DNA (32-mer)
- UniProt
- Q1D4I5
- Ligands
- IVC
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transcriptional regulator, tetr family | protein | 185 | 74% helix, 0% strand | Q1D4I5 |
| B, D | Transcriptional regulator, tetr family | protein | 184 | 73% helix, 0% strand | Q1D4I5 |
| E, F | DNA (32-mer) | dna | 16 | — | — |
Ligands and binding sites
- IVC · Isovaleryl-coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.80 | 0.81 | 102 | IVC |
| 2 | 319 | 0.74 | 0.85 | 33 | IVC |
| 3 | 363 | 0.73 | 0.84 | 36 | IVC |
| 4 | 145 | 0.66 | 0.87 | 26 | empty |
| 5 | 342 | 0.66 | 0.81 | 49 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1468 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1451 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 749 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–C · 364 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 334 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5K7Z · Crystal structure of AibR in complex with isovaleryl coenzyme A and operator DNA · the same entry in another collection · chain A against A, 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 Q1D4I5
- Elsewhere: RCSB PDB 5K7Z · PDBe 5K7Z · UniProt Q1D4I5
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