Research workbench
Crystal structure of TP0037 from treponema pallidum, a D-lactate dehydrogenase
Analyse Crystal structure of TP0037 from treponema pallidum, a D-lactate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JP2
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- O83080
- Ligands
- CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 331 | 40% helix, 17% strand | O83080 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
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 | 211 | 0.69 | 0.86 | 43 | EDO |
| 2 | 442 | 0.69 | 0.80 | 40 | EDO |
| 3 | 465 | 0.66 | 0.78 | 40 | EDO |
| 4 | 154 | 0.50 | 0.79 | 30 | EDO |
| 5 | 180 | 0.47 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2852 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 7JP2 · Crystal structure of TP0037 from Treponema pallidum, a D-lactate dehydrogenase · the same entry in another collection · chain B against B, TM-score 1.00
- O83080 · AlphaFold monomer V2.0 prediction for D-lactate dehydrogenase (O83080) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O83080
- Elsewhere: RCSB PDB 7JP2 · PDBe 7JP2 · UniProt O83080
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