Research workbench
Tryptophan repressor trpr from E.COLI wildtype with indole-3-acetic acid as ligand
Analyse Tryptophan repressor trpr from E.COLI wildtype with indole-3-acetic acid as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EJW
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP operon repressor
- UniProt
- P0A881
- Ligands
- IAC
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | TRP operon repressor | protein | 101 | 81% helix, 0% strand | P0A881 |
Ligands and binding sites
- IAC · 1H-indol-3-ylacetic acid · ligand · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.59 | 0.76 | 31 | empty |
| 2 | 73 | 0.47 | 0.83 | 15 | IAC |
| 3 | 83 | 0.45 | 0.81 | 17 | IAC |
| 4 | 77 | 0.43 | 0.80 | 14 | IAC |
| 5 | 56 | 0.41 | 0.82 | 14 | IAC |
Interfaces
6 interfaces between chains.
- C–D · 2307 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2281 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 82 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6EJW · Tryptophan Repressor TrpR from E.coli wildtype with Indole-3-acetic acid as ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P0A881 · AlphaFold monomer V2.0 prediction for TRP operon repressor (P0A881) · 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 P0A881
- Elsewhere: RCSB PDB 6EJW · PDBe 6EJW · UniProt P0A881
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