MolNFT v1 · #109637 · protein
Crystal structure of a trap periplasmic solute binding protein from rhodobacter sphaeroides (RSPH17029_2138, target efi-510205) with bound glucuronate
4X8R · Trap dicarboxylate transporter, dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from rhodobacter sphaeroides (RSPH17029_2138…”. X-ray diffraction, 2 ligands (BDP, PO4), 7 pockets (best druggability…
- PDB
- 4X8R
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- A3PLM5
- Ligands
- BDP, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trap dicarboxylate transporter, dctp subunit | protein | 304 | 49% helix, 19% strand | A3PLM5 |
Ligands and binding sites
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.72 | 0.97 | 20 | BDP |
| 2 | 57 | 0.69 | 0.97 | 20 | BDP |
| 3 | 403 | 0.65 | 0.79 | 49 | empty |
| 4 | 61 | 0.28 | 0.74 | 13 | empty |
| 5 | 63 | 0.28 | 0.73 | 22 | PO4 |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4X8R · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM Rhodobacter… · 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 A3PLM5
- Elsewhere: RCSB PDB 4X8R · PDBe 4X8R · UniProt A3PLM5
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