Research workbench
Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability
Analyse Comparison of family 12 glycoside hydrolases and recruited substitutions… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OA2
- Type
- protein
- Length
- 1,308 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-1,4-glucanase
- EC
- 3.2.1.4
- UniProt
- O00095
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Endo-beta-1,4-glucanase (EC 3.2.1.4) | protein | 218 | 6% helix, 56% strand | O00095 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.76 | 0.80 | 106 | empty |
| 2 | 495 | 0.70 | 0.80 | 78 | empty |
| 3 | 365 | 0.68 | 0.81 | 50 | NAG |
| 4 | 455 | 0.68 | 0.80 | 60 | NAG |
| 5 | 374 | 0.67 | 0.81 | 52 | empty |
Interfaces
5 interfaces between chains.
- D–E · 999 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 991 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 922 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 319 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 309 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 6 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1OA2 · Comparison of Family 12 Glycoside Hydrolases and Recruited Substitutions Important for… · 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 O00095
- Elsewhere: RCSB PDB 1OA2 · PDBe 1OA2 · UniProt O00095
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