Research workbench
Contribution of disulfide bond toward thermostability in hyperthermostable endocellulase
Analyse Contribution of disulfide bond toward thermostability in hyperthermostable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DM1
- Type
- protein
- Length
- 1,131 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 458AA long hypothetical endo-1,4-beta-glucanase
- EC
- 3.2.1.4
- UniProt
- O58925
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 458AA long hypothetical endo-1,4-beta-glucanase (EC 3.2.1.4) | protein | 377 | 31% helix, 17% strand | O58925 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.77 | 0.82 | 54 | PO4 |
| 2 | 597 | 0.73 | 0.81 | 77 | PO4 |
| 3 | 269 | 0.69 | 0.84 | 44 | PO4 |
| 4 | 131 | 0.54 | 0.82 | 25 | empty |
| 5 | 88 | 0.50 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 719 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 525 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4DM1 · Contribution of disulfide bond toward thermostability in hyperthermostable endocellulase · 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 O58925
- Elsewhere: RCSB PDB 4DM1 · PDBe 4DM1 · UniProt O58925
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