MolNFT v1 · #56796 · protein
T-state structure of allosteric L-lactate dehydrogenase from lactobacillus casei
2ZQY: “T-state structure of allosteric L-lactate dehydrogenase from lactobacillus casei”. X-ray diffraction, 1 ligand (NO3), 16 pockets (best druggability 0.78). MolNFT v1 #56796 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ZQY
- Type
- protein
- Length
- 1,234 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
- P00343
- Ligands
- NO3
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 50% helix, 21% strand | P00343 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 308 | 50% helix, 20% strand | P00343 |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 52% helix, 20% strand | P00343 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.78 | 0.81 | 88 | NO3 |
| 2 | 541 | 0.72 | 0.80 | 61 | NO3 |
| 3 | 568 | 0.71 | 0.79 | 59 | empty |
| 4 | 450 | 0.70 | 0.81 | 51 | NO3 |
| 5 | 518 | 0.69 | 0.79 | 54 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1705 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1700 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 944 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2ZQY · T-state structure of allosteric L-lactate dehydrogenase from Lactobacillus casei · the same entry in another collection · chain A against A, TM-score 1.00
- P00343 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P00343) · a predicted model of the same protein · chain B 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 P00343
- Elsewhere: RCSB PDB 2ZQY · PDBe 2ZQY · UniProt P00343
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