Research workbench
Crystal structure of TT0316 protein from thermus thermophilus HB8
Analyse Crystal structure of TT0316 protein 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
- 2CUK
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerate DEHYDROGENASE/GLYOXYLATE reductase
- EC
- 1.1.1.-
- UniProt
- Q5SMG6
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerate DEHYDROGENASE/GLYOXYLATE reductase (EC 1.1.1.-) | protein | 311 | 34% helix, 16% strand | Q5SMG6 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.75 | 0.82 | 60 | empty |
| 2 | 357 | 0.72 | 0.84 | 40 | empty |
| 3 | 498 | 0.71 | 0.81 | 69 | empty |
| 4 | 347 | 0.69 | 0.82 | 46 | NHE |
| 5 | 446 | 0.68 | 0.79 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3243 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3200 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 331 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 63 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2CUK · Crystal structure of TT0316 protein 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 Q5SMG6
- Elsewhere: RCSB PDB 2CUK · PDBe 2CUK · UniProt Q5SMG6
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