Research workbench
Flavobacterium johnsoniae GH31 dextranase, FJDEX31A
Analyse Flavobacterium johnsoniae GH31 dextranase, FJDEX31A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JR6
- 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
- Pockets
- 20 · best druggability 0.78
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
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.78 | 0.82 | 84 | ACT, MPD |
| 2 | 713 | 0.77 | 0.82 | 81 | ACT, MPD |
| 3 | 862 | 0.76 | 0.80 | 87 | MPD |
| 4 | 526 | 0.66 | 0.77 | 71 | empty |
| 5 | 79 | 0.61 | 0.89 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 979 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 901 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 399 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 262 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6JR6 · Flavobacterium johnsoniae GH31 dextranase, FjDex31A · 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
- Every structure of UniProt A5FBI1
- Elsewhere: RCSB PDB 6JR6 · PDBe 6JR6 · UniProt A5FBI1
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