MolNFT v1 · #21105 · protein + DNA
Crystal structure of transcriptional regulator- phosphoprotein-DNA complex
1RZR · 5'- D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3': “Crystal structure of transcriptional regulator- phosphoprotein-DNA complex”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #21105…
- PDB
- 1RZR
- Type
- protein + DNA
- Length
- 1,740 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'; 5'…
- UniProt
- P46828, O69250
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, E | 5'- D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3' | dna | 16 | — | — |
| R, B | 5'- D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3' | dna | 16 | — | — |
| G, C, A, D | Glucose-resistance amylase regulator | protein | 332 | 48% helix, 14% strand | P46828 |
| T, L, Y, S | Phosphocarrier protein hpr | protein | 87 | 36% helix, 28% strand | O69250 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 7 copies · chains G, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.79 | 0.85 | 74 | empty |
| 2 | 867 | 0.78 | 0.81 | 94 | empty |
| 3 | 785 | 0.77 | 0.81 | 65 | empty |
| 4 | 187 | 0.69 | 0.87 | 30 | empty |
| 5 | 56 | 0.65 | 0.94 | 15 | empty |
Interfaces
20 interfaces between chains.
- G–C · 2179 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 2126 Ų buried · 27 hydrogen bonds · protein-protein
- C–T · 745 Ų buried · 9 hydrogen bonds · protein-protein
- D–Y · 741 Ų buried · 6 hydrogen bonds · protein-protein
- H–R · 729 Ų buried · 76 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 43 modified (engineered, phosphorylation).
Compared structures
- 1RZR · crystal structure of transcriptional regulator-phosphoprotein-DNA complex · the same entry in another collection · chain S against S, 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 P46828
- Every structure of UniProt O69250
- Elsewhere: RCSB PDB 1RZR · PDBe 1RZR · UniProt P46828 · UniProt O69250
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