Research workbench
Structure of the lactate racemase apoprotein from thermoanaerobacterium thermosaccharolyticum
Analyse Structure of the lactate racemase apoprotein from thermoanaerobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJG
- Type
- protein
- Length
- 835 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate racemase apoprotein
- EC
- 5.1.2.1
- UniProt
- D9TQ02
- Ligands
- MG, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate racemase apoprotein (EC 5.1.2.1) | protein | 418 | 37% helix, 26% strand | D9TQ02 |
| B | Lactate racemase apoprotein (EC 5.1.2.1) | protein | 417 | 38% helix, 26% strand | D9TQ02 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.80 | 0.83 | 85 | SO4 |
| 2 | 923 | 0.78 | 0.80 | 92 | SO4, EDO |
| 3 | 156 | 0.42 | 0.74 | 25 | empty |
| 4 | 72 | 0.41 | 0.79 | 21 | empty |
| 5 | 120 | 0.39 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2YJG · Structure of the lactate racemase apoprotein from Thermoanaerobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- D9TQ02 · AlphaFold monomer V2.0 prediction for lactate racemase (D9TQ02) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 D9TQ02
- Elsewhere: RCSB PDB 2YJG · PDBe 2YJG · UniProt D9TQ02
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