MolNFT v1 · #138105 · protein
Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 29 and NADH
5W8K · L-lactate dehydrogenase a chain: “Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 29 and NADH”. X-ray diffraction, 2 ligands (NAI, 9Y7), 20 pockets (best druggability 0.87). MolNFT v1 #138105 on…
- PDB
- 5W8K
- Type
- protein
- Length
- 1,313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Ligands
- NAI, 9Y7
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 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 | 323 | 46% helix, 19% strand | P00338 |
| B, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 18% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 46% helix, 19% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 9Y7 · 2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid · ligand · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, D
- MLA · Malonic acid · additive · 5 copies · chains A, C, B, 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 | 743 | 0.87 | 0.90 | 81 | GOL, MLA |
| 2 | 328 | 0.82 | 0.92 | 42 | MLA, GOL |
| 3 | 250 | 0.72 | 0.87 | 39 | MLA, NAI |
| 4 | 74 | 0.70 | 0.95 | 18 | empty |
| 5 | 55 | 0.66 | 0.96 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2873 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2840 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1696 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1600 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5W8K · Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 and… · the same entry in another collection · chain D against D, TM-score 1.00
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 5W8K · PDBe 5W8K · UniProt P00338
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