Research workbench
Crystal structure of eilr in complex with crystal violet
Analyse Crystal structure of eilr in complex with crystal violet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLM
- Type
- protein
- Length
- 1,513 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein tetr
- UniProt
- E3G817
- Ligands
- CVI
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Regulatory protein tetr | protein | 188 | 75% helix, 0% strand | E3G817 |
| B | Regulatory protein tetr | protein | 189 | 75% helix, 0% strand | E3G817 |
| C | Regulatory protein tetr | protein | 187 | 72% helix, 0% strand | E3G817 |
| D, F, H | Regulatory protein tetr | protein | 191 | 75% helix, 0% strand | E3G817 |
Ligands and binding sites
- CVI · Crystal violet · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.85 | 0.87 | 84 | CVI |
| 2 | 566 | 0.81 | 0.87 | 57 | CVI |
| 3 | 587 | 0.80 | 0.86 | 56 | CVI |
| 4 | 288 | 0.79 | 0.90 | 37 | CVI |
| 5 | 317 | 0.78 | 0.89 | 36 | CVI |
Interfaces
9 interfaces between chains.
- G–H · 1402 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1383 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1360 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1311 Ų buried · 8 hydrogen bonds · protein-protein
- D–G · 845 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5VLM · Crystal structure of EilR in complex with crystal violet · the same entry in another collection · chain D against D, 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 E3G817
- Elsewhere: RCSB PDB 5VLM · PDBe 5VLM · UniProt E3G817
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