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 D- erythronate with residual density suggestive of superposition with copurified alternative ligand.
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
- 4P9K
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- A1WPV4
- Ligands
- EAX
- Pockets
- 3 · best druggability 0.59
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 | 303 | 51% helix, 21% strand | A1WPV4 |
Ligands and binding sites
- EAX · (2R,3R)-2,3,4-trihydroxybutanoic acid · ligand · chains A
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 | 52 | 0.59 | 0.92 | 21 | EAX |
| 2 | 67 | 0.32 | 0.75 | 18 | empty |
| 3 | 71 | 0.29 | 0.73 | 20 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 4P9K · 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 4P9K · PDBe 4P9K · UniProt A1WPV4
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