Research workbench
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase
Analyse Refined crystal structure of dogfish M4 apo-lactate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDH
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M4 apo-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00341
- Ligands
- ACE, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M4 apo-lactate dehydrogenase (EC 1.1.1.27) | protein | 329 | 44% helix, 17% strand | P00341 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.68 | 0.79 | 57 | SO4 |
| 2 | 178 | 0.45 | 0.75 | 26 | SO4 |
| 3 | 78 | 0.33 | 0.75 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6LDH · Refined crystal structure of dogfish M4 apo-lactate dehydrogenase · 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 0.99
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 P00341
- Elsewhere: RCSB PDB 6LDH · PDBe 6LDH · UniProt P00341
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