Research workbench
Two-component response regulator NARL/DNA complex: DNA bending found in a high affinity site
Analyse Two-component response regulator NARL/DNA complex: DNA bending found in a high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JE8
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP *G)-3'; NITRATE/NITRITE…
- UniProt
- P10957
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, G, H | 5'- D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP *G)-3' | dna | 20 | — | — |
| A, B, F | NITRATE/NITRITE response regulator protein narl | protein | 66 | 68% helix, 0% strand | P10957 |
| E | NITRATE/NITRITE response regulator protein narl | protein | 67 | 69% helix, 0% strand | P10957 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains C, D, A, B, H, E, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.56 | 0.78 | 33 | empty |
| 2 | 208 | 0.55 | 0.79 | 34 | empty |
| 3 | 89 | 0.43 | 0.80 | 19 | SO4 |
| 4 | 76 | 0.41 | 0.80 | 20 | SO4 |
| 5 | 90 | 0.40 | 0.78 | 16 | SO4 |
Interfaces
12 interfaces between chains.
- G–H · 962 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- C–D · 961 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–B · 433 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 421 Ų buried · 0 hydrogen bonds · protein-protein
- H–E · 399 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1JE8 · Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity… · the same entry in another collection · chain C against C, 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 P10957
- Elsewhere: RCSB PDB 1JE8 · PDBe 1JE8 · UniProt P10957
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