MolNFT v2 · #227058 · 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 (R-enantiomer, orthorhombic P form)
9BK3 · L-lactate dehydrogenase A chain: “Crystal structure of Lactate dehydrogenase in complex with…”. X-ray diffraction at 2.4, 2 ligands (A1AR0, CL), 20 pockets (best druggability 0.89). MolNFT v2 #227058 on GenesisL1: 3D structure…
- PDB
- 9BK3
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- L-lactate dehydrogenase A chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Ligands
- A1AR0, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 2.4 · 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 | 315 | 47% helix, 20% strand | P00338 |
| B | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 316 | 44% helix, 19% strand | P00338 |
| C | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 330 | 45% helix, 18% strand | P00338 |
| D | L-lactate dehydrogenase A chain (EC 1.1.1.27) | protein | 331 | 46% helix, 18% strand | P00338 |
Ligands and binding sites
- A1AR0 · (2R)-4-[4-(1-methyl-1H-imidazole-2-carbonyl)anilino]-4-oxo-2-[4-(trifluoromethyl)phenyl]butanoic acid · ligand · chains D
- CL · Chloride ion · ion · 4 copies · chains A, C, D, B
- MLI · Malonate ion · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.89 | 0.91 | 119 | CL |
| 2 | 83 | 0.71 | 0.95 | 18 | empty |
| 3 | 179 | 0.68 | 0.87 | 39 | MLI |
| 4 | 196 | 0.67 | 0.86 | 38 | MLI |
| 5 | 63 | 0.65 | 0.94 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2926 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2843 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1623 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1487 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 992 Ų buried · 9 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 9BK3 · PDBe 9BK3 · UniProt P00338
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