Research workbench
Crystal structure of lactate dehydrogenase from eimeria maxima with NADH and oxamate
Analyse Crystal structure of lactate dehydrogenase from eimeria maxima with NADH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CT6
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- UniProt
- U6M598
- Ligands
- NAI, OXM, GLC
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase | protein | 321 | 50% helix, 20% strand | U6M598 |
| B | Lactate dehydrogenase | protein | 331 | 48% helix, 19% strand | U6M598 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains B
- OXM · Oxamic acid · ligand · chains B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.79 | 0.81 | 122 | NAI, OXM |
| 2 | 140 | 0.48 | 0.78 | 22 | empty |
| 3 | 123 | 0.46 | 0.78 | 20 | empty |
| 4 | 159 | 0.42 | 0.74 | 20 | empty |
| 5 | 133 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2059 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6CT6 · Crystal structure of lactate dehydrogenase from Eimeria maxima with NADH and oxamate · the same entry in another collection · chain A against A, TM-score 1.00
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 U6M598
- Elsewhere: RCSB PDB 6CT6 · PDBe 6CT6 · UniProt U6M598
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