Research workbench
Crystal structure of SIGMA54 activator NTRC4'S DNA binding domain
Analyse Crystal structure of SIGMA54 activator NTRC4'S DNA binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E7L
- Type
- protein
- Length
- 237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator (ntrc family)
- UniProt
- O66551
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator (ntrc family) | protein | 60 | 62% helix, 0% strand | O66551 |
| B | Transcriptional regulator (ntrc family) | protein | 54 | 74% helix, 0% strand | O66551 |
| C | Transcriptional regulator (ntrc family) | protein | 60 | 68% helix, 0% strand | O66551 |
| D | Transcriptional regulator (ntrc family) | protein | 63 | 65% helix, 0% strand | O66551 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.32 | 0.77 | 13 | empty |
| 2 | 57 | 0.32 | 0.77 | 17 | empty |
| 3 | 55 | 0.29 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1139 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 82 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3E7L · Crystal structure of sigma54 activator NtrC4's DNA binding domain · 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 O66551
- Elsewhere: RCSB PDB 3E7L · PDBe 3E7L · UniProt O66551
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