Research workbench
Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 29
Analyse Crystal structure of lactate dehydrogenase a in complex with inhibitor compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W8J
- Type
- protein
- Length
- 1,322 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
- 9Y7
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P00338 |
| B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 18% strand | P00338 |
Ligands and binding sites
- 9Y7 · 2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid · ligand · 6 copies · chains A, B, C, D
- MLA · Malonic acid · additive · 5 copies · chains A, C, B, D
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, C, D
- GOL · Glycerol · additive · 2 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.89 | 0.91 | 115 | MLA |
| 2 | 190 | 0.69 | 0.87 | 39 | MLA |
| 3 | 74 | 0.69 | 0.95 | 19 | empty |
| 4 | 66 | 0.66 | 0.94 | 15 | empty |
| 5 | 433 | 0.65 | 0.78 | 48 | 9Y7, DMS |
Interfaces
6 interfaces between chains.
- C–D · 2915 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2875 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1655 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1563 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 957 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5W8J · Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 · the same entry in another collection · chain A against A, 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 5W8J · PDBe 5W8J · UniProt P00338
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