MolNFT v1 · #84935 · protein
5-mutant (R79W, R151A, E279A, E299A,E313A) lactate-dehydrogenase from thermus thermophillus
3ZZN · Lactate dehydrogenase: “5-mutant (R79W, R151A, E279A, E299A,E313A) lactate-dehydrogenase from thermus thermophillus”. X-ray diffraction, 1 ligand (ADP), 17 pockets (best druggability 0.81). MolNFT v1 #84935 on GenesisL1: 3D…
- PDB
- 3ZZN
- Type
- protein
- Length
- 1,240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5SJA1
- Ligands
- ADP
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 49% helix, 24% strand | Q5SJA1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.81 | 0.82 | 80 | empty |
| 2 | 947 | 0.80 | 0.82 | 78 | empty |
| 3 | 521 | 0.68 | 0.78 | 63 | empty |
| 4 | 462 | 0.64 | 0.77 | 51 | empty |
| 5 | 450 | 0.63 | 0.77 | 57 | ADP |
Interfaces
6 interfaces between chains.
- C–D · 1861 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1816 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 871 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZZN · 5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus… · 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 3ZZN · PDBe 3ZZN · UniProt Q5SJA1
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