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Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 23 and zinc
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
- 5W8I
- Type
- protein
- Length
- 1,315 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
- 9YD, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 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 | 328 | 46% helix, 19% strand | P00338 |
Ligands and binding sites
- 9YD · 2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1, 3-thiazole-4-carboxylic acid · ligand · 3 copies · chains A, C, D
- ZN · Zinc ion · metal · 5 copies · chains A, C, B, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
- MLA · Malonic acid · additive · chains B
- GOL · Glycerol · additive · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.89 | 0.91 | 121 | ZN, CIT, DMS |
| 2 | 153 | 0.68 | 0.88 | 30 | MLA |
| 3 | 66 | 0.66 | 0.94 | 15 | empty |
| 4 | 458 | 0.66 | 0.78 | 48 | ZN, 9YD |
| 5 | 482 | 0.65 | 0.77 | 54 | ZN, 9YD |
Interfaces
6 interfaces between chains.
- C–D · 2927 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2871 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1589 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1586 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 961 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5W8I · Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and… · 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 5W8I · PDBe 5W8I · UniProt P00338
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