Research workbench
A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes
Analyse A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LDH
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00341
- Ligands
- ACE, NAD, PYR
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase (EC 1.1.1.27) | protein | 329 | 41% helix, 15% strand | P00341 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- PYR · Pyruvic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.68 | 0.81 | 60 | NAD, PYR |
| 2 | 209 | 0.59 | 0.80 | 24 | empty |
| 3 | 129 | 0.56 | 0.83 | 24 | empty |
| 4 | 78 | 0.37 | 0.76 | 15 | empty |
| 5 | 85 | 0.35 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3LDH · A comparison of the structures of apo dogfish m4 lactate dehydrogenase and its ternary… · the same entry in another collection · chain A against A, TM-score 1.00
- P00341 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P00341) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00341
- Elsewhere: RCSB PDB 3LDH · PDBe 3LDH · UniProt P00341
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