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Crystal structure of leuconostoc citreum nrrl B-1299 dextransucrase dsr-M
Analyse Crystal structure of leuconostoc citreum nrrl B-1299 dextransucrase dsr-M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGY
- Type
- protein
- Length
- 2,409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dsr-M glucansucrase inactive mutant E715Q
- Ligands
- GLC, PR, CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dsr-M glucansucrase inactive mutant E715Q | protein | 1265 | 21% helix, 23% strand | — |
| B | Dsr-M glucansucrase inactive mutant E715Q | protein | 1144 | 23% helix, 21% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- PR · Praseodymium ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
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 | 816 | 0.72 | 0.77 | 69 | empty |
| 2 | 112 | 0.71 | 0.93 | 23 | empty |
| 3 | 730 | 0.71 | 0.78 | 58 | PR |
| 4 | 111 | 0.71 | 0.92 | 25 | empty |
| 5 | 575 | 0.69 | 0.79 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5NGY · Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M · 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
- Elsewhere: RCSB PDB 5NGY · PDBe 5NGY
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