Research workbench
Tandem binding in crystals of a TRP REPRESSOR/OPERATOR half-site complex
Analyse Tandem binding in crystals of a TRP REPRESSOR/OPERATOR half-site complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TRR
- Type
- protein + DNA
- Length
- 896 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)- 3'); Protein (TRP repressor)
- UniProt
- P0A881
- Ligands
- TRP
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, F, I, L | DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)- 3') | dna | 16 | — | — |
| A, B, D, E, G, H, J, K | Protein (TRP repressor) | protein | 104 | 74% helix, 0% strand | P0A881 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 8 copies · chains C, A, B, I, L, D, E, F, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.79 | 0.82 | 96 | TRP |
| 2 | 964 | 0.79 | 0.81 | 106 | TRP |
| 3 | 141 | 0.79 | 0.97 | 22 | empty |
| 4 | 134 | 0.79 | 0.97 | 23 | empty |
| 5 | 132 | 0.77 | 0.96 | 22 | empty |
Interfaces
41 interfaces between chains.
- D–E · 2559 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 2553 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2548 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2545 Ų buried · 18 hydrogen bonds · protein-protein
- F–L · 731 Ų buried · 75 hydrogen bonds · nucleic-nucleic
Compared structures
- 1TRR · Tandem binding in crystals of a TRP REPRESSOR/OPERATOR half-site complex · the same entry in another collection · chain K against K, 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 P0A881
- Elsewhere: RCSB PDB 1TRR · PDBe 1TRR · UniProt P0A881
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