Research workbench
Rat ldha in complex with 2-((4-(2-((3-((2-methyl-1,3-benzothiazol-6- YL)AMINO)-3-oxo-PROPYL)CARBAMOYLAMINO)ETHYL)PHENYL)METHYL) propanedioic acid
Analyse Rat ldha in complex with 2-((4-(2-((3-((2-methyl-1,3-benzothiazol-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AJN
- Type
- protein
- Length
- 1,318 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
- P04642
- Ligands
- 88V
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P04642 |
| B, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 330 | 45% helix, 19% strand | P04642 |
Ligands and binding sites
- 88V · (4-{2-[({3-[(2-methyl-1,3-benzothiazol-6-yl)amino]-3-oxopropyl}carbamoyl)amino]ethyl}benzyl)propanedioic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.89 | 0.91 | 127 | empty |
| 2 | 193 | 0.70 | 0.88 | 35 | 88V |
| 3 | 241 | 0.70 | 0.86 | 39 | 88V |
| 4 | 226 | 0.68 | 0.85 | 37 | 88V |
| 5 | 214 | 0.67 | 0.85 | 39 | 88V |
Interfaces
6 interfaces between chains.
- C–D · 2905 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2880 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1652 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1630 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 963 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4AJN · rat LDHA in complex with 2-((4-(2-((3-((2-methyl-1,3-benzothiazol-6… · the same entry in another collection · chain C against C, TM-score 1.00
- P04642 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P04642) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P04642
- Elsewhere: RCSB PDB 4AJN · PDBe 4AJN · UniProt P04642
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