MolNFT v1 · #103386 · protein
Crystal structure of a trap periplasmic solute binding protein from sulfitobacter sp. nas-14.1 (target efi-510299) with bound beta-D- galacturonate
4PF8 · Trap-T family transporter, dctp (periplasmic binding)…: “Crystal structure of a trap periplasmic solute binding protein from sulfitobacter sp. nas-14.1 (target…”. X-ray diffraction, 2 ligands (GTR, CL), 3 pockets (best druggability…
- PDB
- 4PF8
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap-T family transporter, dctp (periplasmic binding) subunit
- UniProt
- A3T0C3
- Ligands
- GTR, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap-T family transporter, dctp (periplasmic binding) subunit | protein | 300 | 52% helix, 18% strand | A3T0C3 |
| B | Trap-T family transporter, dctp (periplasmic binding) subunit | protein | 300 | 52% helix, 19% strand | A3T0C3 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 574 | 0.75 | 0.82 | 90 | CL, GTR |
| 2 | 99 | 0.34 | 0.73 | 22 | empty |
| 3 | 63 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1025 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4PF8 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp.… · 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 A3T0C3
- Elsewhere: RCSB PDB 4PF8 · PDBe 4PF8 · UniProt A3T0C3
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