Research workbench
Crystal structure of the N-terminal domain of sucrase-isomaltase
Analyse Crystal structure of the N-terminal domain of sucrase-isomaltase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LPO
- Type
- protein
- Length
- 3,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrase-isomaltase
- EC
- 3.2.1.10
- UniProt
- P14410
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sucrase-isomaltase (EC 3.2.1.10) | protein | 870 | 21% helix, 30% strand | P14410 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.99 | 20 | empty |
| 2 | 71 | 0.75 | 0.99 | 21 | empty |
| 3 | 75 | 0.75 | 0.98 | 20 | empty |
| 4 | 67 | 0.74 | 0.99 | 23 | empty |
| 5 | 81 | 0.74 | 0.97 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–C · 778 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 207 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 3LPO · Crystal structure of the N-terminal domain of sucrase-isomaltase · the same entry in another collection · chain A against A, TM-score 1.00
- P14410 · AlphaFold monomer V2.0 prediction for sucrase-isomaltase, intestinal (P14410) · a predicted model of the same protein · 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 P14410
- Elsewhere: RCSB PDB 3LPO · PDBe 3LPO · UniProt P14410
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