Research workbench
Crystal structure of human lactate dehydrogenase a with inhibitor compound 15
Analyse Crystal structure of human lactate dehydrogenase a with inhibitor compound 15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M2N
- Type
- protein
- Length
- 1,320 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, YOJ, SO4
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 46% helix, 19% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 21% strand | P00338 |
| C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 19% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- YOJ · 5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl) methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 75 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.89 | 0.91 | 115 | SO4, EDO, PEG, GOL |
| 2 | 848 | 0.73 | 0.78 | 78 | EDO, NAI, PEG, YOJ |
| 3 | 846 | 0.73 | 0.77 | 74 | NAI, YOJ, EDO |
| 4 | 80 | 0.72 | 0.95 | 19 | empty |
| 5 | 81 | 0.70 | 0.94 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2906 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2900 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1723 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1670 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 992 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7M2N · Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15 · 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 7M2N · PDBe 7M2N · UniProt P00338
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