Research workbench
Structural study of project id TTHB049 from thermus thermophilus HB8 (L19M)
Analyse Structural study of project id TTHB049 from thermus thermophilus HB8 (L19M) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EKB
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ribazole-5'-phosphate phosphatase
- UniProt
- Q53WB3
- Ligands
- NA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ribazole-5'-phosphate phosphatase | protein | 171 | 37% helix, 17% strand | Q53WB3 |
| B | Alpha-ribazole-5'-phosphate phosphatase | protein | 170 | 39% helix, 17% strand | Q53WB3 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.68 | 0.82 | 30 | empty |
| 2 | 273 | 0.67 | 0.83 | 30 | empty |
| 3 | 71 | 0.54 | 0.86 | 25 | empty |
| 4 | 69 | 0.49 | 0.84 | 18 | empty |
| 5 | 84 | 0.33 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 717 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2EKB · Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M) · 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 Q53WB3
- Elsewhere: RCSB PDB 2EKB · PDBe 2EKB · UniProt Q53WB3
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