Research workbench
Sco glgei-V279S in complex with 4-alpha-glucoside of validamine
Analyse Sco glgei-V279S in complex with 4-alpha-glucoside of validamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEL
- Type
- protein
- Length
- 1,298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,4-GLUCAN:MALTOSE-1-phosphate maltosyltransferase 1
- EC
- 2.4.99.16
- UniProt
- Q9L1K2
- Ligands
- Z3D, CL
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-1,4-GLUCAN:MALTOSE-1-phosphate maltosyltransferase 1 (EC 2.4.99.16) | protein | 649 | 34% helix, 25% strand | Q9L1K2 |
Ligands and binding sites
- Z3D · (1R,2R,3S,4S,6R)-4-amino-2,3-dihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.76 | 0.81 | 57 | empty |
| 2 | 709 | 0.74 | 0.80 | 52 | empty |
| 3 | 938 | 0.73 | 0.77 | 83 | empty |
| 4 | 278 | 0.70 | 0.85 | 34 | Z3D, CL |
| 5 | 259 | 0.68 | 0.84 | 32 | Z3D, CL |
Interfaces
1 interface between chains.
- A–B · 2215 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7MEL · Sco GlgEI-V279S in complex with 4-alpha-glucoside of validamine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9L1K2 · AlphaFold monomer V2.0 prediction for alpha-1,4-GLUCAN:MALTOSE-1-phosphate… · a predicted model of the same protein · 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 Q9L1K2
- Elsewhere: RCSB PDB 7MEL · PDBe 7MEL · UniProt Q9L1K2
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