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The crystal structure of glycosyl hydrolase family 2 (GH2) member from bacteroides cellulosilyticus dsm 14838
Analyse The crystal structure of glycosyl hydrolase family 2 (GH2) member from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B6L
- Type
- protein
- Length
- 1,453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 2, sugar binding domain protein
- UniProt
- E2N721
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 2, sugar binding domain protein | protein | 727 | 15% helix, 41% strand | E2N721 |
| B | Glycosyl hydrolase family 2, sugar binding domain protein | protein | 726 | 16% helix, 41% strand | E2N721 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 3 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.79 | 0.87 | 72 | empty |
| 2 | 390 | 0.75 | 0.85 | 51 | empty |
| 3 | 401 | 0.72 | 0.83 | 37 | EDO, FMT |
| 4 | 442 | 0.71 | 0.82 | 35 | empty |
| 5 | 426 | 0.71 | 0.82 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 729 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered, oxidation).
Compared structures
- 6B6L · The crystal structure of glycosyl hydrolase family 2 (GH2) member from Bacteroides… · 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 E2N721
- Elsewhere: RCSB PDB 6B6L · PDBe 6B6L · UniProt E2N721
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