MolNFT v2 · #227057 · protein
Crystal structure of Lactate dehydrogenase in complex with 4-((4-(1-methyl-1H-imidazole-2-carbonyl)phenyl)amino)-4-oxo-2-(4-(trifluoromethyl)phenyl)butanoic acid (S-enantiomer, monoclinic P form)
9BK2 · L-lactate dehydrogenase A chain: “Crystal structure of Lactate dehydrogenase in complex with…”. X-ray diffraction at 1.85, 1 ligand (A1AQ0), 19 pockets (best druggability 0.89). MolNFT v2 #227057 on GenesisL1: 3D structure, binding…
- PDB
- 9BK2
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- L-lactate dehydrogenase A chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Ligands
- A1AQ0
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · resolution 1.85 · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 328 | 47% helix, 19% strand | P00338 |
| B | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P00338 |
| C | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P00338 |
| D | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 330 | 45% helix, 19% strand | P00338 |
Ligands and binding sites
- A1AQ0 · (2S)-4-[4-(1-methyl-1H-imidazole-2-carbonyl)anilino]-4-oxo-2-[4-(trifluoromethyl)phenyl]butanoic acid · ligand · chains A, D
- MLI · Malonate ion · additive · 10 copies · chains A, D, B, C
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.89 | 0.91 | 121 | DMS, MLI |
| 2 | 66 | 0.69 | 0.96 | 16 | empty |
| 3 | 57 | 0.67 | 0.95 | 14 | empty |
| 4 | 122 | 0.65 | 0.89 | 30 | MLI |
| 5 | 143 | 0.61 | 0.85 | 39 | MLI |
Interfaces
6 interfaces between chains.
- A–C · 2874 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2852 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1720 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 987 Ų buried · 8 hydrogen bonds · protein-protein
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 P00338
- Elsewhere: RCSB PDB 9BK2 · PDBe 9BK2 · UniProt P00338
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