MolNFT v1 · #141797 · protein
Lactate dehydrogenase with NADH and mla
5ZJD · L-lactate dehydrogenase a chain: “Lactate dehydrogenase with NADH and mla”. X-ray diffraction, 1 ligand (NAI), 20 pockets (best druggability 0.89). MolNFT v1 #141797 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZJD
- Type
- protein
- Length
- 2,648 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 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 · 8 copies · chains A, B, C, D, E, F, G, H
- MLI · Malonate ion · additive · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1073 | 0.89 | 0.91 | 125 | empty |
| 2 | 809 | 0.88 | 0.91 | 92 | empty |
| 3 | 334 | 0.83 | 0.93 | 55 | empty |
| 4 | 197 | 0.74 | 0.90 | 28 | NAI, MLI |
| 5 | 310 | 0.74 | 0.86 | 47 | NAI, MLI |
Interfaces
12 interfaces between chains.
- C–D · 2923 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2902 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2886 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2836 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1753 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5ZJD · Lactate dehydrogenase with NADH and 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 5ZJD · PDBe 5ZJD · UniProt P00338
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