Research workbench
Crystal structure of ABC transporter substrate-binding protein from sinorhizobium meliloti
Analyse Crystal structure of ABC transporter substrate-binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WED
- Type
- protein
- Length
- 483 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, periplasmic solute-binding protein
- UniProt
- Q92YH7
- Ligands
- NA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, periplasmic solute-binding protein | protein | 483 | 27% helix, 23% strand | Q92YH7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · chains A
- GOL · Glycerol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.64 | 0.78 | 46 | empty |
| 2 | 149 | 0.63 | 0.86 | 25 | empty |
| 3 | 311 | 0.61 | 0.78 | 48 | NA, FMT, GOL |
| 4 | 297 | 0.55 | 0.76 | 38 | empty |
| 5 | 222 | 0.55 | 0.78 | 30 | empty |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4WED · Crystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti · 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 Q92YH7
- Elsewhere: RCSB PDB 4WED · PDBe 4WED · UniProt Q92YH7
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