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
- 2LDB
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00344
- Ligands
- NAD, FBP, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 301 | 42% helix, 21% strand | P00344 |
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 B, C, A, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.82 | 0.91 | 49 | FBP |
| 2 | 341 | 0.81 | 0.91 | 50 | FBP |
| 3 | 88 | 0.62 | 0.89 | 22 | SO4 |
| 4 | 91 | 0.61 | 0.89 | 21 | SO4 |
| 5 | 217 | 0.60 | 0.81 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2116 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 2113 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 991 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 991 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 692 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2LDB · Structure determination and refinement of bacillus stearothermophilus lactate… · the same entry in another collection · chain A against A, 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 2LDB · PDBe 2LDB · UniProt P00344
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