MolNFT v1 · #97806 · protein
Crystal structure of yeast glycogen synthase in complex with uridine- 5'-monophosphate
4KQ1 · GSY2P: “Crystal structure of yeast glycogen synthase in complex with uridine- 5'-monophosphate”. X-ray diffraction, 2 ligands (U5P, G6P), 20 pockets (best druggability 0.77). MolNFT v1 #97806 on GenesisL1: 3D structure, binding…
- PDB
- 4KQ1
- Type
- protein
- Length
- 2,550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GSY2P
- EC
- 2.4.1.11
- UniProt
- E7NKU1
- Ligands
- U5P, G6P
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GSY2P (EC 2.4.1.11) | protein | 638 | 50% helix, 15% strand | E7NKU1 |
| D | GSY2P (EC 2.4.1.11) | protein | 636 | 49% helix, 14% strand | E7NKU1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.77 | 0.80 | 76 | U5P |
| 2 | 805 | 0.73 | 0.78 | 81 | U5P |
| 3 | 720 | 0.71 | 0.78 | 58 | U5P |
| 4 | 449 | 0.70 | 0.81 | 56 | empty |
| 5 | 416 | 0.69 | 0.81 | 46 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1666 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1651 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 795 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 789 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4KQ1 · Crystal structure of yeast glycogen synthase in complex with uridine-5'-monophosphate · 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 E7NKU1
- Elsewhere: RCSB PDB 4KQ1 · PDBe 4KQ1 · UniProt E7NKU1
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