Research workbench
Crystal structure of ecmrr C-terminal domain
Analyse Crystal structure of ecmrr C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WL5
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecmrr transcriptional regulator
- Ligands
- 16A, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ecmrr transcriptional regulator | protein | 158 | 23% helix, 41% strand | — |
Ligands and binding sites
- 16A · Cetyl-trimethyl-ammonium · ligand · 10 copies · chains A, B, D, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.75 | 0.80 | 42 | 16A |
| 2 | 688 | 0.75 | 0.80 | 41 | 16A |
| 3 | 611 | 0.72 | 0.80 | 66 | 16A, GOL, EDO |
| 4 | 208 | 0.65 | 0.84 | 27 | 16A, GOL |
| 5 | 205 | 0.63 | 0.83 | 28 | 16A, GOL |
Interfaces
3 interfaces between chains.
- B–C · 811 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 777 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 517 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6WL5 · Crystal structure of EcmrR C-terminal domain · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6WL5 · PDBe 6WL5
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