MolNFT v1 · #145610 · protein
Crystal structure of lactate dehydrogenase from eimeria maxima with NADH and oxamate
6CT6: “Crystal structure of lactate dehydrogenase from eimeria maxima with NADH and oxamate”. X-ray diffraction, 3 ligands (NAI, OXM, GLC), 10 pockets (best druggability 0.79). MolNFT v1 #145610 on GenesisL1: 3D structure, binding sites…
- 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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