Research workbench
Crystal structure of 2-O-alpha-glucosylglycerol phosphorylase in complex with isofagomine and glycerol
Analyse Crystal structure of 2-O-alpha-glucosylglycerol phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KTR
- Type
- protein
- Length
- 6,090 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 65 central catalytic
- EC
- 2.4.1.-
- UniProt
- D6XZ22
- Ligands
- IFM, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Glycoside hydrolase family 65 central catalytic (EC 2.4.1.-) | protein | 762 | 33% helix, 25% strand | D6XZ22 |
| B, C, D, E, F, H | Glycoside hydrolase family 65 central catalytic (EC 2.4.1.-) | protein | 761 | 33% helix, 28% strand | D6XZ22 |
Ligands and binding sites
- IFM · 5-hydroxymethyl-3,4-dihydroxypiperidine · ligand · 6 copies · chains A, D, E, F, G, H
- CA · Calcium ion · metal · 7 copies · chains A, F, B, D, C, H, E, G
- GOL · Glycerol · additive · 44 copies · chains A, F, C, B, D, E, G, H
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, F, G
- PG4 · Tetraethylene glycol · additive · 4 copies · chains B, D, F, H
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, C, E
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, E
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 2 copies · chains B, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains C
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.80 | 0.94 | 31 | GOL |
| 2 | 135 | 0.80 | 0.97 | 28 | GOL |
| 3 | 202 | 0.80 | 0.94 | 42 | IFM, GOL |
| 4 | 908 | 0.79 | 0.82 | 90 | IFM, GOL, CA |
| 5 | 819 | 0.79 | 0.82 | 87 | IFM, GOL, CA |
Interfaces
13 interfaces between chains.
- G–H · 1539 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1513 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1509 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1498 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KTR · Crystal structure of 2-O-alpha-glucosylglycerol phosphorylase in complex with isofagomine… · the same entry in another collection · chain H against H, TM-score 1.00
- D6XZ22 · AlphaFold monomer V2.0 prediction for 1,2-alpha-glucosylglycerol phosphorylase (D6XZ22) · a predicted model of the same protein · chain H 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 D6XZ22
- Elsewhere: RCSB PDB 4KTR · PDBe 4KTR · UniProt D6XZ22
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