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The crystal structure of the E. COLI maltodextrin phosphorylase complex
Analyse The crystal structure of the E. COLI maltodextrin phosphorylase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ECP
- 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
- AC1, PLP, GLC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltodextrin phosphorylase (EC 2.4.1.1) | protein | 796 | 54% helix, 14% strand | P00490 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · 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 | 1185 | 0.81 | 0.82 | 79 | empty |
| 2 | 1196 | 0.79 | 0.80 | 108 | GLC, AC1, GOL, PLP |
| 3 | 1063 | 0.78 | 0.80 | 91 | GLC, AC1, GOL, PLP |
| 4 | 554 | 0.70 | 0.79 | 43 | empty |
| 5 | 578 | 0.69 | 0.79 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 2102 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2ECP · The crystal structure of the E. COLI maltodextrin phosphorylase complex · 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 2ECP · PDBe 2ECP · UniProt P00490
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