Research workbench
Crystal structure of a predicted DNA-binding transcriptional regulator (SARO_1072) from novosphingobium aromaticivorans dsm at 1.85 a resolution
Analyse Crystal structure of a predicted DNA-binding transcriptional regulator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QTQ
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, tetr family
- UniProt
- Q2G9F6
- Ligands
- NO3
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, tetr family | protein | 204 | 77% helix, 1% strand | Q2G9F6 |
| B, C | Transcriptional regulator, tetr family | protein | 197 | 81% helix, 1% strand | Q2G9F6 |
| D | Transcriptional regulator, tetr family | protein | 198 | 79% helix, 1% strand | Q2G9F6 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.81 | 0.88 | 73 | EDO |
| 2 | 125 | 0.71 | 0.91 | 29 | EDO |
| 3 | 235 | 0.65 | 0.83 | 22 | NO3 |
| 4 | 293 | 0.53 | 0.75 | 30 | empty |
| 5 | 81 | 0.35 | 0.76 | 16 | EDO |
Interfaces
3 interfaces between chains.
- C–D · 1940 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1934 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2QTQ · Crystal structure of a predicted dna-binding transcriptional regulator (saro_1072) from… · 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 Q2G9F6
- Elsewhere: RCSB PDB 2QTQ · PDBe 2QTQ · UniProt Q2G9F6 · AlphaFold DB Q2G9F6
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