Research workbench
The structure of a putative MALATE/LACTATE dehydrogenase from E. COLI.
Analyse The structure of a putative MALATE/LACTATE dehydrogenase from E. COLI. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G8Y
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALATE/L-lactate dehydrogenases
- UniProt
- P30178
- Ligands
- NAD, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALATE/L-lactate dehydrogenases | protein | 359 | 45% helix, 20% strand | P30178 |
| B | MALATE/L-lactate dehydrogenases | protein | 358 | 45% helix, 18% strand | P30178 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.79 | 0.84 | 69 | SO4, NAD, EDO |
| 2 | 616 | 0.78 | 0.84 | 69 | SO4, NAD, EDO |
| 3 | 110 | 0.37 | 0.74 | 18 | empty |
| 4 | 70 | 0.33 | 0.75 | 18 | empty |
| 5 | 76 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3508 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2G8Y · The structure of a putative malate/lactate dehydrogenase from E. coli. · the same entry in another collection · chain A against A, TM-score 1.00
- P30178 · AlphaFold monomer V2.0 prediction for hydroxycarboxylate dehydrogenase B (P30178) · a predicted model of the same protein · 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 P30178
- Elsewhere: RCSB PDB 2G8Y · PDBe 2G8Y · UniProt P30178
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