MolNFT v1 · #13259 · protein
Crystal structure of the maltodextrin phosphorylase complexed with the products of the enzymatic reaction between glucose-1-phosphate and maltotetraose
1L5W: “Crystal structure of the maltodextrin phosphorylase complexed with the products of the enzymatic reaction…”. X-ray diffraction, 3 ligands (PLP, GLC, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #13259 on GenesisL1: 3D…
- PDB
- 1L5W
- Type
- protein
- Length
- 1,592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin phosphorylase
- EC
- 2.4.1.1
- Ligands
- PLP, GLC, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltodextrin phosphorylase (EC 2.4.1.1) | protein | 796 | 53% helix, 14% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.84 | 0.85 | 73 | empty |
| 2 | 625 | 0.82 | 0.87 | 87 | GLC, PO4, PLP |
| 3 | 660 | 0.81 | 0.86 | 85 | GLC, PO4, PLP |
| 4 | 56 | 0.73 | 1.00 | 17 | empty |
| 5 | 52 | 0.72 | 0.99 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2174 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1L5W · Crystal Structure of the Maltodextrin Phosphorylase Complexed with the Products of the… · 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
- Elsewhere: RCSB PDB 1L5W · PDBe 1L5W
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