MolNFT v1 · #141401 · protein
Crystal structure of sugar-binding protein yeso in complex with rhamnogalacturonan trisaccharide
5Z6B · Putative ABC transporter substrate-binding protein yeso: “Crystal structure of sugar-binding protein yeso in complex with rhamnogalacturonan trisaccharide”. X-ray diffraction, 3 ligands (GAD, RAM, GAL), 3 pockets (best druggability…
- PDB
- 5Z6B
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ABC transporter substrate-binding protein yeso
- UniProt
- O31518
- Ligands
- GAD, RAM, GAL
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ABC transporter substrate-binding protein yeso | protein | 393 | 50% helix, 14% strand | O31518 |
Ligands and binding sites
- GAD · 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid · ligand · chains A
- RAM · alpha-L-rhamnopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · 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 | 893 | 0.83 | 0.85 | 87 | RAM, GAD, GAL |
| 2 | 88 | 0.46 | 0.80 | 22 | empty |
| 3 | 62 | 0.36 | 0.78 | 17 | empty |
Compared structures
- 5Z6B · Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan… · the same entry in another collection · chain A against A, TM-score 1.00
- O31518 · AlphaFold monomer V2.0 prediction for putative ABC transporter substrate-binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.76
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 O31518
- Elsewhere: RCSB PDB 5Z6B · PDBe 5Z6B · UniProt O31518
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