Research workbench
Crystal structure of minor L-lactate dehydrogenase from enterococcus mundtii in the ligands-unbound 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
- 3WSV
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 312 | 41% helix, 19% strand | — |
| B, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 317 | 41% helix, 19% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.84 | 0.87 | 66 | GOL |
| 2 | 753 | 0.84 | 0.87 | 65 | GOL |
| 3 | 605 | 0.76 | 0.82 | 57 | empty |
| 4 | 702 | 0.74 | 0.80 | 52 | empty |
| 5 | 275 | 0.73 | 0.87 | 42 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1628 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1605 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1179 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1151 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1079 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3WSV · 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 3WSV · PDBe 3WSV
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