Research workbench
Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole and phosphate in the T and R states
Analyse Complex of glycogen phosphorylase with a transition state analogue nojirimycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NOI
- Type
- protein
- Length
- 3,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, NTZ, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycogen phosphorylase (EC 2.4.1.1) | protein | 823 | 51% helix, 13% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- NTZ · Nojirimycine tetrazole · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.83 | 0.85 | 91 | PO4, PLP, NTZ |
| 2 | 1116 | 0.83 | 0.84 | 80 | empty |
| 3 | 949 | 0.83 | 0.84 | 75 | empty |
| 4 | 1055 | 0.82 | 0.83 | 101 | PO4, PLP, NTZ |
| 5 | 514 | 0.81 | 0.87 | 79 | PO4, PLP, NTZ |
Interfaces
6 interfaces between chains.
- A–B · 2606 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2455 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 862 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 828 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 363 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1NOI · Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole… · 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 P00489
- Elsewhere: RCSB PDB 1NOI · PDBe 1NOI · UniProt P00489
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