Research workbench
Crystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (BAM_6123), target efi-510059, with bound beta-D-galacturonate
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
- 4N17
- Type
- protein
- Length
- 301 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q0B2F6
- Ligands
- GTR, CA, CL
- Pockets
- 2 · best druggability 0.65
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 | 301 | 51% helix, 19% strand | Q0B2F6 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.65 | 0.93 | 23 | GTR, CL |
| 2 | 79 | 0.37 | 0.77 | 22 | empty |
Compared structures
- 4N17 · Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0B2F6 · AlphaFold monomer V2.0 prediction for solute-binding protein BAMB_6123 (Q0B2F6) · 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 Q0B2F6
- Elsewhere: RCSB PDB 4N17 · PDBe 4N17 · UniProt Q0B2F6
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