Research workbench
Rat ldha in complex with 4-((2-allylsulfanyl-1,3-benzothizol-6-yl) amino)-4-oxo-butanoic acid
Analyse Rat ldha in complex with 4-((2-allylsulfanyl-1,3-benzothizol-6-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AJ4
- 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
- P04642
- Ligands
- VAB
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 330 | 45% helix, 18% strand | P04642 |
Ligands and binding sites
- VAB · 4-oxo-4-{[2-(prop-2-en-1-ylsulfanyl)-1,3-benzothiazol-6-yl]amino}butanoic acid · ligand · 4 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 8 copies · chains A, D, B, C
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 | 981 | 0.89 | 0.91 | 113 | MLI |
| 2 | 90 | 0.73 | 0.96 | 24 | MLI |
| 3 | 63 | 0.67 | 0.95 | 14 | empty |
| 4 | 187 | 0.66 | 0.86 | 37 | MLI, VAB |
| 5 | 57 | 0.65 | 0.95 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2908 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2904 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1686 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 960 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4AJ4 · rat LDHA in complex with 4-((2-allylsulfanyl-1,3-benzothizol-6-yl) amino)-4-oxo-butanoic… · the same entry in another collection · chain A against A, 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 A 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 4AJ4 · PDBe 4AJ4 · UniProt P04642
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