Research workbench
Crystal structure of glucocerebrosidase in complex with a pyrrolopyrazine
Analyse Crystal structure of glucocerebrosidase in complex with a pyrrolopyrazine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T13
- Type
- protein
- Length
- 1,985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- B2R6A7
- Ligands
- M7H, NAG, SO4, CL
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 28% helix, 28% strand | B2R6A7 |
| D | Glucosylceramidase (EC 3.2.1.45) | protein | 494 | 27% helix, 28% strand | B2R6A7 |
Ligands and binding sites
- M7H · 1-[4-[2-(4-methoxyphenyl)-5-methyl-pyrrolo[2,3-b]pyrazin-6-yl]piperidin-1-yl]ethanone · ligand · 2 copies · chains B, C, A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, D, B, C
- CL · Chloride ion · ion · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.87 | 0.88 | 110 | EDO |
| 2 | 505 | 0.83 | 0.89 | 53 | TRS, M7H |
| 3 | 504 | 0.83 | 0.89 | 56 | TRS, M7H |
| 4 | 465 | 0.70 | 0.81 | 50 | empty |
| 5 | 300 | 0.67 | 0.82 | 49 | GOL, EDO |
Interfaces
5 interfaces between chains.
- A–C · 1137 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 1016 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 922 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 890 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6T13 · Crystal structure of glucocerebrosidase in complex with a pyrrolopyrazine · 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 B2R6A7
- Elsewhere: RCSB PDB 6T13 · PDBe 6T13 · UniProt B2R6A7
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