MolNFT v1 · #30768 · protein
Crystal structure of lactate dehydrogenase from plasmodium vivax: complex with NADH
2A92 · L-lactate dehydrogenase: “Crystal structure of lactate dehydrogenase from plasmodium vivax: complex with NADH”. X-ray diffraction, 1 ligand (NAI), 19 pockets (best druggability 0.83). MolNFT v1 #30768 on GenesisL1: 3D structure…
- PDB
- 2A92
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- Ligands
- NAI
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 48% helix, 20% strand | — |
| B, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 50% helix, 20% strand | — |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 318 | 47% helix, 20% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.83 | 0.97 | 43 | empty |
| 2 | 186 | 0.82 | 0.97 | 46 | empty |
| 3 | 1192 | 0.82 | 0.83 | 68 | empty |
| 4 | 508 | 0.76 | 0.84 | 65 | NAI |
| 5 | 676 | 0.76 | 0.81 | 62 | NAI |
Interfaces
6 interfaces between chains.
- A–C · 2190 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 2180 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1273 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 778 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2A92 · Crystal structure of lactate dehydrogenase from Plasmodium vivax: complex with NADH · 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
- Elsewhere: RCSB PDB 2A92 · PDBe 2A92
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