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Rabbit muscle glycogen phosphorylase B in complex with N-(2-naphthoyl) -N-beta-D-glucopyranosyl urea determined at 2.0 a resolution
Analyse Rabbit muscle glycogen phosphorylase B in complex with N-(2-naphthoyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZCT
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- VMP, PLP, IMP
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- VMP · N-[[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]carbamoyl]naphthalene-2-carboxamide · ligand · 2 copies · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- IMP · Inosinic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.86 | 0.93 | 57 | PLP, VMP |
| 2 | 136 | 0.78 | 0.96 | 43 | empty |
| 3 | 450 | 0.69 | 0.81 | 58 | empty |
| 4 | 205 | 0.53 | 0.77 | 27 | IMP |
| 5 | 102 | 0.51 | 0.82 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3ZCT · Rabbit muscle glycogen phosphorylase b in complex with N-(2-naphthoyl)… · 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 3ZCT · PDBe 3ZCT · UniProt P00489
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