Research workbench
Tryptophan repressor trpr from E.COLI variant S88Y with indole-3- acetic acid as ligand
Analyse Tryptophan repressor trpr from E.COLI variant S88Y with indole-3- acetic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EJZ
- Type
- protein
- Length
- 408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP operon repressor
- UniProt
- B7LEN9
- Ligands
- IAC, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRP operon repressor | protein | 103 | 81% helix, 0% strand | B7LEN9 |
| B, C | TRP operon repressor | protein | 102 | 80% helix, 0% strand | B7LEN9 |
| D | TRP operon repressor | protein | 101 | 81% helix, 0% strand | B7LEN9 |
Ligands and binding sites
- IAC · 1H-indol-3-ylacetic acid · ligand · 5 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · chains C, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.66 | 0.75 | 47 | EDO, IAC |
| 2 | 119 | 0.48 | 0.79 | 25 | IAC, EDO |
| 3 | 83 | 0.47 | 0.82 | 17 | IAC, EDO |
| 4 | 79 | 0.47 | 0.82 | 20 | IAC, EDO |
| 5 | 89 | 0.47 | 0.81 | 20 | IAC, EDO |
Interfaces
5 interfaces between chains.
- A–C · 2338 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 2318 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6EJZ · Tryptophan Repressor TrpR from E.coli variant S88Y with Indole-3-acetic acid as ligand · the same entry in another collection · chain A against A, TM-score 1.00
- B7LEN9 · AlphaFold monomer V2.0 prediction for TRP operon repressor (B7LEN9) · a predicted model of the same protein · chain D 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 B7LEN9
- Elsewhere: RCSB PDB 6EJZ · PDBe 6EJZ · UniProt B7LEN9
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