MolNFT v1 · #137584 · protein
Sco glgei-V279S in complex with a pyrolidene-based methyl-phosphonate compound
5VT4 · Alpha-1,4-GLUCAN:MALTOSE-1-phosphate maltosyltransferase 1: “Sco glgei-V279S in complex with a pyrolidene-based methyl-phosphonate compound”. X-ray diffraction, 1 ligand (9KJ), 20 pockets (best druggability 0.77). MolNFT v1 #137584…
- PDB
- 5VT4
- Type
- protein
- Length
- 2,580 residues
- Chains
- 4
- 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
- 9KJ
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 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 | 648 | 34% helix, 25% strand | Q9L1K2 |
| C | Alpha-1,4-GLUCAN:MALTOSE-1-phosphate maltosyltransferase 1 (EC 2.4.99.16) | protein | 635 | 33% helix, 25% strand | Q9L1K2 |
| D | 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
- 9KJ · {[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid · ligand · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.77 | 0.82 | 53 | empty |
| 2 | 1177 | 0.77 | 0.79 | 91 | 9KJ |
| 3 | 848 | 0.76 | 0.79 | 54 | empty |
| 4 | 881 | 0.73 | 0.77 | 85 | empty |
| 5 | 1154 | 0.72 | 0.76 | 102 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2256 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2144 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VT4 · Sco GlgEI-V279S in complex with a pyrolidene-based methyl-phosphonate compound · the same entry in another collection · chain D against D, 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 5VT4 · PDBe 5VT4 · UniProt Q9L1K2
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