Research workbench
Crystal structure of TTHA1563 from thermus thermophilus HB8
Analyse Crystal structure of TTHA1563 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z1K
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (NEO)PULLULANASE
- EC
- 3.2.1.41
- UniProt
- Q5SI17
- Ligands
- GLC, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | (NEO)PULLULANASE (EC 3.2.1.41) | protein | 474 | 34% helix, 18% strand | Q5SI17 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 40 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.78 | 0.83 | 63 | empty |
| 2 | 1163 | 0.77 | 0.79 | 106 | empty |
| 3 | 474 | 0.73 | 0.83 | 43 | PO4 |
| 4 | 310 | 0.69 | 0.83 | 41 | empty |
| 5 | 236 | 0.67 | 0.84 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 880 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 800 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 250 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 161 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 2Z1K · Crystal Structure of Ttha1563 from Thermus thermophilus HB8 · 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 Q5SI17
- Elsewhere: RCSB PDB 2Z1K · PDBe 2Z1K · UniProt Q5SI17
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