Research workbench
Effector binding domain of quir in complex with shikimate
Analyse Effector binding domain of quir in complex with shikimate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TED
- Type
- protein
- Length
- 428 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO0488 protein; His tag peptide
- UniProt
- Q8Y9N7
- Ligands
- SKM
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | LMO0488 protein | protein | 210 | 36% helix, 31% strand | Q8Y9N7 |
| A | LMO0488 protein | protein | 209 | 35% helix, 31% strand | Q8Y9N7 |
| H | His tag peptide | protein | 9 | 44% helix, 0% strand | — |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 18 | SKM |
| 2 | 283 | 0.67 | 0.83 | 41 | empty |
| 3 | 177 | 0.48 | 0.76 | 36 | empty |
| 4 | 131 | 0.43 | 0.76 | 21 | empty |
| 5 | 64 | 0.39 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1239 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 360 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TED · Effector binding domain of QuiR in complex with shikimate · the same entry in another collection · chain B against B, 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 Q8Y9N7
- Elsewhere: RCSB PDB 5TED · PDBe 5TED · UniProt Q8Y9N7
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