Research workbench
Flavobacterium johnsoniae GH31 dextranase, FJDEX31A, complexed with glucose
Analyse Flavobacterium johnsoniae GH31 dextranase, FJDEX31A, complexed with glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JR7
- Type
- protein
- Length
- 3,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Candidate alpha-glycosidase glycoside hydrolase family 31
- EC
- 3.2.1.20
- UniProt
- A5FBI1
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Candidate alpha-glycosidase glycoside hydrolase family 31 (EC 3.2.1.20) | protein | 812 | 22% helix, 30% strand | A5FBI1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.77 | 0.79 | 91 | MPD |
| 2 | 1064 | 0.76 | 0.79 | 87 | MPD |
| 3 | 777 | 0.75 | 0.80 | 68 | MPD |
| 4 | 331 | 0.63 | 0.79 | 43 | GLC, ACT |
| 5 | 357 | 0.63 | 0.79 | 45 | GLC, ACT |
Interfaces
4 interfaces between chains.
- C–D · 975 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 891 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6JR7 · Flavobacterium johnsoniae GH31 dextranase, FjDex31A, complexed with glucose · the same entry in another collection · chain D against D, 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 A5FBI1
- Elsewhere: RCSB PDB 6JR7 · PDBe 6JR7 · UniProt A5FBI1
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