Research workbench
Crystal structure of TTHA0849 from thermus thermophilus HB8
Analyse Crystal structure of TTHA0849 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
- 2D4R
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TTHA0849
- UniProt
- Q5SK03
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hypothetical protein TTHA0849 | protein | 146 | 28% helix, 47% strand | Q5SK03 |
| C | Hypothetical protein TTHA0849 | protein | 145 | 29% helix, 49% strand | Q5SK03 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.86 | 0.87 | 120 | SO4 |
| 2 | 107 | 0.60 | 0.86 | 25 | empty |
| 3 | 133 | 0.44 | 0.76 | 17 | empty |
| 4 | 144 | 0.44 | 0.75 | 17 | empty |
| 5 | 70 | 0.43 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 585 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 442 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 411 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 314 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2D4R · Crystal structure of TTHA0849 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 Q5SK03
- Elsewhere: RCSB PDB 2D4R · PDBe 2D4R · UniProt Q5SK03
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