Research workbench
Crystal structure of the hypothetical protein (GK1056) from geobacillus kaustophilus HTA426
Analyse Crystal structure of the hypothetical protein (GK1056) from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYH
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical conserved protein, GK1056
- UniProt
- Q5L139
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical conserved protein, GK1056 | protein | 256 | 39% helix, 23% strand | Q5L139 |
| B | Hypothetical conserved protein, GK1056 | protein | 258 | 39% helix, 23% strand | Q5L139 |
| D | Hypothetical conserved protein, GK1056 | protein | 257 | 38% helix, 23% strand | Q5L139 |
Ligands and binding sites
- GOL · Glycerol · additive · 16 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.79 | 0.81 | 84 | GOL |
| 2 | 962 | 0.79 | 0.81 | 82 | GOL |
| 3 | 536 | 0.66 | 0.77 | 74 | GOL |
| 4 | 275 | 0.61 | 0.79 | 45 | empty |
| 5 | 304 | 0.57 | 0.77 | 38 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1175 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1065 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1060 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 2QYH · Crystal structure of the hypothetical protein (gk1056) from geobacillus kaustophilus… · 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 Q5L139
- Elsewhere: RCSB PDB 2QYH · PDBe 2QYH · UniProt Q5L139
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