Research workbench
Penta mutant of lactate dehydrogenase from thermus thermophilus, ternary complex
Analyse Penta mutant of lactate dehydrogenase from thermus thermophilus, ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XXJ
- Type
- protein
- Length
- 1,239 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5SJA1
- Ligands
- OXM, NAD, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 48% helix, 24% strand | Q5SJA1 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 309 | 49% helix, 21% strand | Q5SJA1 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 2 copies · chains B, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.85 | 0.88 | 71 | SO4 |
| 2 | 675 | 0.82 | 0.86 | 60 | SO4 |
| 3 | 600 | 0.68 | 0.77 | 64 | empty |
| 4 | 550 | 0.67 | 0.77 | 68 | empty |
| 5 | 172 | 0.66 | 0.86 | 33 | OXM, NAD |
Interfaces
6 interfaces between chains.
- A–B · 2016 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1982 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1097 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1093 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2XXJ · Penta mutant of lactate dehydrogenase from Thermus thermophilus, ternary complex · 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 2XXJ · PDBe 2XXJ · UniProt Q5SJA1
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