Research workbench
Crystal structure of the ligand binding domain of E. COLI iclr.
Analyse Crystal structure of the ligand binding domain of E. COLI iclr. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TD5
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetate operon repressor
- UniProt
- P16528
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetate operon repressor | protein | 179 | 41% helix, 23% strand | P16528 |
| C | Acetate operon repressor | protein | 178 | 40% helix, 25% strand | P16528 |
| D | Acetate operon repressor | protein | 180 | 41% helix, 23% strand | P16528 |
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 | 998 | 0.70 | 0.74 | 71 | empty |
| 2 | 73 | 0.47 | 0.82 | 18 | empty |
| 3 | 104 | 0.41 | 0.76 | 16 | empty |
| 4 | 57 | 0.39 | 0.80 | 18 | empty |
| 5 | 54 | 0.34 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 630 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 182 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 1TD5 · Crystal Structure of the Ligand Binding Domain of E. coli IclR. · the same entry in another collection · chain A against A, TM-score 1.00
- P16528 · AlphaFold monomer V2.0 prediction for transcriptional repressor iclr (P16528) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P16528
- Elsewhere: RCSB PDB 1TD5 · PDBe 1TD5 · UniProt P16528
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