Research workbench
Crystal structure of leucine-rich protein regulator, elrr, from enterococcus faecalis
Analyse Crystal structure of leucine-rich protein regulator, elrr, from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V5T
- Type
- protein
- Length
- 1,213 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved domain protein
- UniProt
- Q830T5
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved domain protein | protein | 306 | 73% helix, 1% strand | Q830T5 |
| B | Conserved domain protein | protein | 305 | 73% helix, 1% strand | Q830T5 |
| C | Conserved domain protein | protein | 300 | 74% helix, 1% strand | Q830T5 |
| D | Conserved domain protein | protein | 302 | 72% helix, 1% strand | Q830T5 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.79 | 0.97 | 27 | empty |
| 2 | 108 | 0.78 | 0.96 | 22 | empty |
| 3 | 509 | 0.71 | 0.80 | 49 | empty |
| 4 | 484 | 0.71 | 0.81 | 50 | empty |
| 5 | 582 | 0.71 | 0.79 | 63 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4121 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 4082 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 575 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified (engineered).
Compared structures
- 5V5T · Crystal structure of leucine-rich protein regulator, ElrR, from Enterococcus faecalis · 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
- Every structure of UniProt Q830T5
- Elsewhere: RCSB PDB 5V5T · PDBe 5V5T · UniProt Q830T5
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