Research workbench
Crystal structure of TRP repressor operator complex at atomic resolution
Analyse Crystal structure of TRP repressor operator complex at atomic resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TRO
- Type
- protein + DNA
- Length
- 477 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3'); Protein (TRP…
- UniProt
- P0A881
- Ligands
- TRP
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J, K, L | DNA (5'- D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3') | dna | 19 | — | — |
| A | Protein (TRP repressor) | protein | 104 | 82% helix, 0% strand | P0A881 |
| C | Protein (TRP repressor) | protein | 99 | 81% helix, 0% strand | P0A881 |
| E | Protein (TRP repressor) | protein | 97 | 80% helix, 0% strand | P0A881 |
| G | Protein (TRP repressor) | protein | 101 | 82% helix, 0% strand | P0A881 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains J, A, C, I, L, E, G, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.74 | 0.82 | 59 | empty |
| 2 | 589 | 0.73 | 0.81 | 48 | empty |
| 3 | 66 | 0.57 | 0.89 | 17 | TRP |
| 4 | 61 | 0.56 | 0.89 | 14 | TRP |
| 5 | 199 | 0.54 | 0.79 | 31 | TRP |
Interfaces
15 interfaces between chains.
- A–C · 2372 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 2219 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 821 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- K–L · 818 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- I–A · 493 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1TRO · Crystal structure of TRP repressor operator complex at atomic resolution · the same entry in another collection · chain C against C, TM-score 1.00
- P0A881 · AlphaFold monomer V2.0 prediction for TRP operon repressor (P0A881) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P0A881
- Elsewhere: RCSB PDB 1TRO · PDBe 1TRO · UniProt P0A881
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