MolNFT v1 · #137566 · protein
Sco glgei-V279S in complex with a pyrolidene-based ethyl-phosphonate compound
5VSJ · Alpha-1,4-GLUCAN:MALTOSE-1-phosphate maltosyltransferase 1: “Sco glgei-V279S in complex with a pyrolidene-based ethyl-phosphonate compound”. X-ray diffraction, 1 ligand (9HV), 12 pockets (best druggability 0.79). MolNFT v1 #137566…
- PDB
- 5VSJ
- 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
- 9HV
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% 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 | 33% helix, 25% strand | Q9L1K2 |
Ligands and binding sites
- 9HV · {2-[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]ethyl}phosphonic acid · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.79 | 0.81 | 83 | 9HV |
| 2 | 838 | 0.75 | 0.79 | 53 | empty |
| 3 | 1152 | 0.73 | 0.76 | 118 | empty |
| 4 | 308 | 0.70 | 0.84 | 39 | 9HV |
| 5 | 170 | 0.56 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2283 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5VSJ · Sco GlgEI-V279S in complex with a pyrolidene-based ethyl-phosphonate compound · 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 B 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 5VSJ · PDBe 5VSJ · UniProt Q9L1K2
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