Research workbench
Structure of TT368 protein from thermus thermophilus HB8
Analyse Structure of TT368 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
- 1WP4
- Type
- protein
- Length
- 1,154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyisobutyrate dehydrogenase
- EC
- 1.1.1.31
- UniProt
- Q5SLQ6
- Ligands
- NDP, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 288 | 55% helix, 14% strand | Q5SLQ6 |
| C, D | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 289 | 57% helix, 14% strand | Q5SLQ6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.69 | 0.81 | 49 | SO4, NDP |
| 2 | 406 | 0.69 | 0.81 | 51 | SO4, NDP |
| 3 | 401 | 0.68 | 0.80 | 50 | SO4, NDP |
| 4 | 453 | 0.64 | 0.77 | 44 | SO4, NDP |
| 5 | 178 | 0.45 | 0.75 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2620 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2541 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1WP4 · Structure of TT368 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 Q5SLQ6
- Elsewhere: RCSB PDB 1WP4 · PDBe 1WP4 · UniProt Q5SLQ6
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