MolNFT v1 · #99933 · protein
Crystal structure of a trap periplasmic solute binding protein from polaromonas sp. JS666 (BPRO_3107), target efi-510173, with bound ALPHA/BETA D-galacturonate, space group P21
4MIJ · Trap dicarboxylate transporter, dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from polaromonas sp. JS666 (BPRO_3107), target…”. X-ray diffraction, 3 ligands (GTR, ADA, CL), 4 pockets (best…
- PDB
- 4MIJ
- Type
- protein
- Length
- 302 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q128M1
- Ligands
- GTR, ADA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 302 | 51% helix, 19% strand | Q128M1 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · chains A
- ADA · alpha-D-galactopyranuronic acid · sugar · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.67 | 0.95 | 23 | CL, GTR, ADA |
| 2 | 67 | 0.37 | 0.78 | 13 | empty |
| 3 | 60 | 0.37 | 0.79 | 13 | empty |
| 4 | 78 | 0.35 | 0.75 | 20 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4MIJ · Crystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. JS666… · the same entry in another collection · chain A against A, TM-score 1.00
- Q128M1 · AlphaFold monomer V2.0 prediction for solute-binding protein BPRO_3107 (Q128M1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q128M1
- Elsewhere: RCSB PDB 4MIJ · PDBe 4MIJ · UniProt Q128M1
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