MolNFT v1 · #29677 · protein + DNA
Narl complexed to narg-89 promoter palindromic tail-to-tail DNA site
1ZG5 · 5'- D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP…: “Narl complexed to narg-89 promoter palindromic tail-to-tail DNA site”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.60). MolNFT v1 #29677 on…
- PDB
- 1ZG5
- 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*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP *G)-3'; NITRATE/NITRITE…
- UniProt
- P0AF28
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, G, H | 5'- D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP *G)-3' | dna | 20 | — | — |
| A, B, F | NITRATE/NITRITE response regulator protein narl | protein | 66 | 70% helix, 0% strand | P0AF28 |
| E | NITRATE/NITRITE response regulator protein narl | protein | 67 | 70% helix, 0% strand | P0AF28 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, D, B, G, H, E, 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 | 275 | 0.60 | 0.79 | 34 | empty |
| 2 | 243 | 0.59 | 0.80 | 29 | empty |
| 3 | 85 | 0.44 | 0.80 | 18 | SO4 |
| 4 | 101 | 0.43 | 0.78 | 21 | SO4 |
| 5 | 68 | 0.42 | 0.81 | 16 | SO4 |
Interfaces
12 interfaces between chains.
- C–D · 947 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- G–H · 942 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–B · 449 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 431 Ų buried · 0 hydrogen bonds · protein-protein
- H–E · 396 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1ZG5 · NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site · the same entry in another collection · chain F against F, TM-score 1.00
- P0AF28 · AlphaFold monomer V2.0 prediction for NITRATE/NITRITE response regulator protein narl… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0AF28
- Elsewhere: RCSB PDB 1ZG5 · PDBe 1ZG5 · UniProt P0AF28
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