MolNFT v1 · #54706 · protein
Penta-mutant of thermus thermophilus lactate dehydrogenase, complex with AMP
2XXB · L-lactate dehydrogenase: “Penta-mutant of thermus thermophilus lactate dehydrogenase, complex with AMP”. X-ray diffraction, 1 ligand (AMP), 6 pockets (best druggability 0.67). MolNFT v1 #54706 on GenesisL1: 3D structure, binding…
- PDB
- 2XXB
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5SJA1
- Ligands
- AMP
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 47% helix, 22% strand | Q5SJA1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.67 | 0.77 | 56 | AMP |
| 2 | 462 | 0.65 | 0.77 | 61 | AMP |
| 3 | 274 | 0.56 | 0.77 | 28 | empty |
| 4 | 265 | 0.54 | 0.76 | 28 | empty |
| 5 | 60 | 0.32 | 0.76 | 14 | AMP |
Interfaces
1 interface between chains.
- A–B · 1818 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2XXB · Penta-mutant of Thermus thermophilus lactate dehydrogenase, complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJA1 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (Q5SJA1) · 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 Q5SJA1
- Elsewhere: RCSB PDB 2XXB · PDBe 2XXB · UniProt Q5SJA1
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