Research workbench
Crystal structure of the conserved hypothetical protein TT1679 from thermus thermophilus
Analyse Crystal structure of the conserved hypothetical protein TT1679 from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V8D
- Type
- protein
- Length
- 562 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein (TT1679)
- UniProt
- Q72L49
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein (TT1679) | protein | 189 | 36% helix, 26% strand | Q72L49 |
| B | Hypothetical protein (TT1679) | protein | 185 | 36% helix, 27% strand | Q72L49 |
| C | Hypothetical protein (TT1679) | protein | 188 | 38% helix, 27% strand | Q72L49 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.49 | 0.75 | 27 | empty |
| 2 | 199 | 0.46 | 0.74 | 26 | empty |
| 3 | 184 | 0.45 | 0.74 | 21 | empty |
| 4 | 85 | 0.43 | 0.79 | 19 | empty |
| 5 | 97 | 0.41 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 992 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 946 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 818 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1V8D · Crystal structure of the conserved hypothetical protein TT1679 from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q72L49 · AlphaFold monomer V2.0 prediction for UPF0340 protein TT_C0214 (Q72L49) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q72L49
- Elsewhere: RCSB PDB 1V8D · PDBe 1V8D · UniProt Q72L49
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