Research workbench
Structure of TT0471 protein from Thermus thermophilus
Analyse Structure of TT0471 protein from Thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E37
- Type
- protein
- Length
- 2,454 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Thermus thermophilus
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5SJA1
- Ligands
- NAD, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.3 · 5 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, H | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 308 | 47% helix, 21% strand | Q5SJA1 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 304 | 49% helix, 24% strand | Q5SJA1 |
| C, G | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 49% helix, 21% strand | Q5SJA1 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 302 | 48% helix, 23% strand | Q5SJA1 |
| E | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 304 | 49% helix, 24% strand | Q5SJA1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, E, G
- SO4 · Sulfate ion · ion · 2 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.83 | 0.85 | 108 | NAD |
| 2 | 1142 | 0.82 | 0.83 | 158 | NAD |
| 3 | 941 | 0.81 | 0.83 | 78 | empty |
| 4 | 863 | 0.80 | 0.83 | 73 | empty |
| 5 | 520 | 0.76 | 0.83 | 62 | empty |
Interfaces
14 interfaces between chains.
- E–F · 1855 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1816 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1804 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1773 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 963 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
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 Q5SJA1
- Elsewhere: RCSB PDB 2E37 · PDBe 2E37 · UniProt Q5SJA1
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