Research workbench
Crystal structure of a trap periplasmic solute binding protein from desulfovibrio vulgaris (DEVAL_0042, target efi-510114) bound to copurified (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
- 4XEQ
- Type
- protein
- Length
- 1,211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- E3ILJ0
- Ligands
- PAF
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 303 | 52% helix, 18% strand | E3ILJ0 |
| B | Trap dicarboxylate transporter, dctp subunit | protein | 304 | 53% helix, 20% strand | E3ILJ0 |
| C, D | Trap dicarboxylate transporter, dctp subunit | protein | 302 | 51% helix, 20% strand | E3ILJ0 |
Ligands and binding sites
- PAF · Pantoate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.81 | 0.82 | 93 | empty |
| 2 | 56 | 0.72 | 0.98 | 21 | PAF |
| 3 | 63 | 0.72 | 0.97 | 21 | PAF |
| 4 | 53 | 0.71 | 0.98 | 20 | PAF |
| 5 | 394 | 0.62 | 0.77 | 41 | empty |
Interfaces
4 interfaces between chains.
- C–D · 571 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 126 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4XEQ · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO… · 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 E3ILJ0
- Elsewhere: RCSB PDB 4XEQ · PDBe 4XEQ · UniProt E3ILJ0
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