MolNFT v1 · #84432 · protein
Structure of the xylo-oligosaccharide specific solute binding protein from bifidobacterium animalis subsp. lactis bl-04 in complex with xylotriose
3ZKL · Putative sugar transporter solute-binding protein: “Structure of the xylo-oligosaccharide specific solute binding protein from bifidobacterium animalis subsp.…”. X-ray diffraction, 1 ligand (XYP), 3 pockets (best druggability 0.80).…
- PDB
- 3ZKL
- Type
- protein
- Length
- 396 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar transporter solute-binding protein
- UniProt
- C6A6Z1
- Ligands
- XYP
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sugar transporter solute-binding protein | protein | 396 | 48% helix, 16% strand | C6A6Z1 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 3 copies · chains A
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
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 | 468 | 0.80 | 0.87 | 50 | XYP |
| 2 | 179 | 0.44 | 0.74 | 27 | empty |
| 3 | 55 | 0.39 | 0.81 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZKL · Structure of the xylo-oligosaccharide specific solute binding protein from… · 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 C6A6Z1
- Elsewhere: RCSB PDB 3ZKL · PDBe 3ZKL · UniProt C6A6Z1
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