Research workbench
Crystal structure of L-lactate dehydrogenase from cyprinus carpio
Analyse Crystal structure of L-lactate dehydrogenase from cyprinus carpio in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V6A
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- Q9W7K5
- Ligands
- GLC
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 332 | 45% helix, 17% strand | Q9W7K5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.68 | 0.76 | 66 | empty |
| 2 | 455 | 0.64 | 0.77 | 62 | GLC |
| 3 | 408 | 0.62 | 0.77 | 60 | GLC |
| 4 | 93 | 0.36 | 0.74 | 16 | empty |
| 5 | 86 | 0.32 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1V6A · Crystal Structure of L-lactate dehydrogenase from Cyprinus carpio · the same entry in another collection · chain A against A, TM-score 1.00
- Q9W7K5 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (Q9W7K5) · a predicted model of the same protein · chain A 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 Q9W7K5
- Elsewhere: RCSB PDB 1V6A · PDBe 1V6A · UniProt Q9W7K5
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