Research workbench
Crystal structure of non-allosteric L-lactate dehydrogenase from lactobacillus pentosus at 2.3 ångström resolution
Analyse Crystal structure of non-allosteric L-lactate dehydrogenase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EZ4
- Type
- protein
- Length
- 1,250 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P56511
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lactate dehydrogenase (EC 1.1.1.27) | protein | 307 | 52% helix, 21% strand | P56511 |
| B, D | Lactate dehydrogenase (EC 1.1.1.27) | protein | 318 | 51% helix, 20% strand | P56511 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.85 | 0.90 | 82 | empty |
| 2 | 361 | 0.81 | 0.91 | 39 | empty |
| 3 | 457 | 0.64 | 0.77 | 50 | NAD |
| 4 | 441 | 0.64 | 0.77 | 50 | NAD |
| 5 | 196 | 0.59 | 0.81 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2114 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2099 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1067 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 648 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1EZ4 · Crystal structure of non-allosteric L-lactate dehydrogenase from lactobacillus pentosus… · the same entry in another collection · chain A against A, TM-score 1.00
- P56511 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P56511) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P56511
- Elsewhere: RCSB PDB 1EZ4 · PDBe 1EZ4 · UniProt P56511
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