Research workbench
Crystal structure of a trap periplasmic solute binding protein from verminephrobacter eiseniae EF01-2 (VEIS_3954, target efi-510324) a nephridial symbiont of the earthworm eisenia foetida, bound to (R)- pantoic acid
Analyse Crystal structure of a trap periplasmic solute 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
- 4PAK
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- A1WPV4
- Ligands
- PAF, SO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 304 | 51% helix, 21% strand | A1WPV4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.35 | 0.78 | 16 | empty |
| 2 | 53 | 0.24 | 0.72 | 12 | SO4 |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4PAK · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER… · the same entry in another collection · chain A against A, TM-score 1.00
- A1WPV4 · AlphaFold monomer V2.0 prediction for solute-binding protein VEIS_3954 (A1WPV4) · a predicted model of the same protein · 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 A1WPV4
- Elsewhere: RCSB PDB 4PAK · PDBe 4PAK · UniProt A1WPV4
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