Research workbench
Structure determination and refinement of bacillus stearothermophilus lactate dehydrogenase
Analyse Structure determination and refinement of bacillus stearothermophilus lactate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LDB
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo-L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00344
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Apo-L-lactate dehydrogenase (EC 1.1.1.27) | protein | 294 | 43% helix, 19% strand | P00344 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.83 | 0.92 | 53 | empty |
| 2 | 159 | 0.77 | 0.94 | 25 | empty |
| 3 | 195 | 0.75 | 0.91 | 32 | SO4 |
| 4 | 104 | 0.64 | 0.90 | 25 | empty |
| 5 | 100 | 0.64 | 0.90 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2148 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2121 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 982 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 982 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 646 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1LDB · Structure determination and refinement of bacillus stearothermophilus lactate… · the same entry in another collection · chain B against B, TM-score 1.00
- P00344 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P00344) · 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 P00344
- Elsewhere: RCSB PDB 1LDB · PDBe 1LDB · UniProt P00344
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