Research workbench
Crystal structure of minor L-lactate dehydrogenase from enterococcus mundtii in the ligands-bound form
Analyse Crystal structure of minor L-lactate dehydrogenase from enterococcus mundtii in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSW
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- Ligands
- NAD, FBP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 49% helix, 19% strand | — |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 313 | 50% helix, 19% strand | — |
| C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 314 | 52% helix, 19% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.87 | 0.90 | 78 | FBP |
| 2 | 357 | 0.82 | 0.92 | 38 | FBP |
| 3 | 714 | 0.72 | 0.79 | 61 | NAD |
| 4 | 741 | 0.70 | 0.77 | 67 | NAD |
| 5 | 580 | 0.65 | 0.76 | 58 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 2529 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2513 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1145 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1132 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3WSW · Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the… · 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
- Elsewhere: RCSB PDB 3WSW · PDBe 3WSW
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