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YGSY2P in complex with small molecule
Analyse YGSY2P in complex with small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U77
- Type
- protein
- Length
- 2,546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen [starch] synthase isoform 2
- EC
- 2.4.1.11
- UniProt
- P27472
- Ligands
- VMC, G6P
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 638 | 51% helix, 15% strand | P27472 |
| C | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 646 | 49% helix, 14% strand | P27472 |
| D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 624 | 48% helix, 15% strand | P27472 |
Ligands and binding sites
- VMC · 2-methoxy-4-(1-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}-4-phenyl-1H-imidazol-5-yl)phenol · ligand · 3 copies · chains A, C, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 5 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.71 | 0.77 | 75 | VMC |
| 2 | 722 | 0.71 | 0.78 | 75 | empty |
| 3 | 724 | 0.70 | 0.77 | 70 | VMC |
| 4 | 640 | 0.69 | 0.77 | 69 | empty |
| 5 | 669 | 0.68 | 0.76 | 82 | VMC |
Interfaces
6 interfaces between chains.
- A–C · 1657 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1643 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 796 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 733 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P27472
- Elsewhere: RCSB PDB 6U77 · PDBe 6U77 · UniProt P27472
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