Research workbench
Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.
Analyse Starch phosphorylase: structural studies explain oxyanion-dependent kinetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C4M
- Type
- protein
- Length
- 3,154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- Q8KQ56
- Ligands
- PLP, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glycogen phosphorylase (EC 2.4.1.1) | protein | 788 | 54% helix, 14% strand | Q8KQ56 |
| B | Glycogen phosphorylase (EC 2.4.1.1) | protein | 788 | 54% helix, 14% strand | Q8KQ56 |
| C | Glycogen phosphorylase (EC 2.4.1.1) | protein | 790 | 55% helix, 14% strand | Q8KQ56 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D
- FMT · Formic acid · additive · 19 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
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 | 974 | 0.85 | 0.86 | 106 | PO4 |
| 2 | 1095 | 0.83 | 0.84 | 106 | PO4 |
| 3 | 843 | 0.80 | 0.83 | 73 | PLP |
| 4 | 704 | 0.79 | 0.83 | 64 | PLP, PO4 |
| 5 | 997 | 0.79 | 0.80 | 72 | PLP, PO4, FMT |
Interfaces
6 interfaces between chains.
- C–D · 2886 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2876 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 551 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2C4M · Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and… · 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 Q8KQ56
- Elsewhere: RCSB PDB 2C4M · PDBe 2C4M · UniProt Q8KQ56
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