Research workbench
Crystal structure of trex from sulfolobus solfataricus in complex with acarbose intermediate and glucose
Analyse Crystal structure of trex from sulfolobus solfataricus in complex with acarbose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VR5
- Type
- protein
- Length
- 1,429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen operon protein glgx
- EC
- 3.2.1.-
- UniProt
- P95868
- Ligands
- A16, GLC, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen operon protein glgx (EC 3.2.1.-) | protein | 715 | 23% helix, 20% strand | P95868 |
| B | Glycogen operon protein glgx (EC 3.2.1.-) | protein | 714 | 24% helix, 20% strand | P95868 |
Ligands and binding sites
- A16 · 4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.77 | 0.79 | 88 | empty |
| 2 | 1061 | 0.76 | 0.78 | 86 | empty |
| 3 | 531 | 0.67 | 0.78 | 55 | GLC, A16 |
| 4 | 592 | 0.67 | 0.77 | 52 | GLC, A16 |
| 5 | 174 | 0.52 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1483 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2VR5 · Crystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose… · 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 P95868
- Elsewhere: RCSB PDB 2VR5 · PDBe 2VR5 · UniProt P95868
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