Research workbench
X-ray studies on maltodextrin phosphorylase (malp) complexes: recognition of substrates and catalytic mechanism of phosphorylase family
Analyse X-ray studies on maltodextrin phosphorylase (malp) complexes: recognition of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AZD
- 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
- UniProt
- P00490
- Ligands
- PLP, GLC, BGC, VO4
- 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 | P00490 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 959 | 0.84 | 0.85 | 76 | empty |
| 2 | 1194 | 0.79 | 0.81 | 109 | GLC, VO4, PLP, TRS |
| 3 | 1164 | 0.78 | 0.80 | 111 | GLC, VO4, PLP, TRS |
| 4 | 57 | 0.73 | 0.99 | 18 | empty |
| 5 | 50 | 0.72 | 1.00 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2125 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2AZD · X-Ray studies on Maltodextrin Phosphorylase (MalP) Complexes: recognition of substrates… · the same entry in another collection · chain A against A, TM-score 1.00
- P00490 · AlphaFold monomer V2.0 prediction for maltodextrin phosphorylase (P00490) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00490
- Elsewhere: RCSB PDB 2AZD · PDBe 2AZD · UniProt P00490
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