Research workbench
Complex structure of lactobacillus casei lactate dehydrogenase with fructose-1,6-bisphosphate
Analyse Complex structure of lactobacillus casei lactate dehydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J9T
- Type
- protein
- Length
- 1,875 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- S6C1Z0
- Ligands
- FBP, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 52% helix, 20% strand | S6C1Z0 |
| B, F | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 51% helix, 20% strand | S6C1Z0 |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 311 | 52% helix, 20% strand | S6C1Z0 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 314 | 50% helix, 20% strand | S6C1Z0 |
| E | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 308 | 51% helix, 20% strand | S6C1Z0 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 3 copies · chains B, D, E, C, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
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 | 516 | 0.82 | 0.89 | 73 | FBP |
| 2 | 490 | 0.82 | 0.89 | 68 | FBP |
| 3 | 762 | 0.75 | 0.80 | 54 | SO4 |
| 4 | 1056 | 0.72 | 0.76 | 90 | SO4 |
| 5 | 412 | 0.64 | 0.78 | 52 | SO4 |
Interfaces
9 interfaces between chains.
- C–E · 1962 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1935 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1930 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1122 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1119 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6J9T · Complex structure of Lactobacillus casei lactate dehydrogenase with… · 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
- Every structure of UniProt S6C1Z0
- Elsewhere: RCSB PDB 6J9T · PDBe 6J9T · UniProt S6C1Z0
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