Research workbench
The apo-form structure of PTLIC16A from paecilomyces thermophila
Analyse The apo-form structure of PTLIC16A from paecilomyces thermophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDT
- Type
- protein
- Length
- 1,189 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,3-1,4-glucanase
- EC
- 3.2.1.73
- UniProt
- E0XN39
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,3-1,4-glucanase (EC 3.2.1.73) | protein | 298 | 17% helix, 36% strand | E0XN39 |
| B, C, D | Beta-1,3-1,4-glucanase (EC 3.2.1.73) | protein | 297 | 16% helix, 37% strand | E0XN39 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.76 | 0.78 | 107 | empty |
| 2 | 711 | 0.75 | 0.80 | 72 | empty |
| 3 | 289 | 0.56 | 0.76 | 32 | empty |
| 4 | 198 | 0.47 | 0.75 | 30 | empty |
| 5 | 92 | 0.40 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 494 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 230 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3WDT · The apo-form structure of PtLic16A from Paecilomyces thermophila · 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 E0XN39
- Elsewhere: RCSB PDB 3WDT · PDBe 3WDT · UniProt E0XN39
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