Research workbench
Crystal structure of solute binding protein of ABC transporter from rhodopseudomonas palustris BISB5 in complex with vanillic acid
Analyse Crystal structure of solute binding protein of ABC transporter from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EYG
- Type
- protein
- Length
- 727 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twin-arginine translocation pathway signal
- UniProt
- Q13AR6
- Ligands
- VNL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twin-arginine translocation pathway signal | protein | 363 | 42% helix, 26% strand | Q13AR6 |
| B | Twin-arginine translocation pathway signal | protein | 364 | 43% helix, 26% strand | Q13AR6 |
Ligands and binding sites
- VNL · 4-hydroxy-3-methoxybenzoate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.68 | 0.75 | 64 | empty |
| 2 | 61 | 0.30 | 0.75 | 14 | empty |
| 3 | 61 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4EYG · Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas… · 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 Q13AR6
- Elsewhere: RCSB PDB 4EYG · PDBe 4EYG · UniProt Q13AR6
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