MolNFT v1 · #60735 · protein
Crystal structure of lactate dehydrogenase from staphylococcus aureus
3D0O · L-lactate dehydrogenase 1: “Crystal structure of lactate dehydrogenase from staphylococcus aureus”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #60735 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3D0O
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase 1
- EC
- 1.1.1.27
- UniProt
- Q5HJD7
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 309 | 50% helix, 20% strand | Q5HJD7 |
| B | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 310 | 50% helix, 20% strand | Q5HJD7 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.77 | 0.81 | 69 | empty |
| 2 | 443 | 0.64 | 0.77 | 49 | empty |
| 3 | 411 | 0.62 | 0.77 | 50 | empty |
| 4 | 115 | 0.39 | 0.75 | 23 | empty |
| 5 | 53 | 0.36 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 883 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3D0O · Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HJD7 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase 1 (Q5HJD7) · a predicted model of the same protein · chain B 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 Q5HJD7
- Elsewhere: RCSB PDB 3D0O · PDBe 3D0O · UniProt Q5HJD7
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