MolNFT v1 · #141798 · protein
LDHA-MLA
5ZJE · L-lactate dehydrogenase a chain: “LDHA-MLA”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #141798 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZJE
- Type
- protein
- Length
- 3,972 residues
- Chains
- 12
- 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
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 43% helix, 20% strand | P00338 |
Ligands and binding sites
- MLI · Malonate ion · additive · 6 copies · chains A, D, E, G, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.89 | 0.90 | 118 | empty |
| 2 | 1033 | 0.89 | 0.91 | 121 | empty |
| 3 | 689 | 0.86 | 0.90 | 80 | empty |
| 4 | 400 | 0.83 | 0.92 | 49 | empty |
| 5 | 535 | 0.77 | 0.84 | 69 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2896 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2880 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2859 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 2858 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 2834 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZJE · LDHA-mla · 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 5ZJE · PDBe 5ZJE · UniProt P00338
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