MolNFT v1 · #128455 · protein
Rabbit muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate
5NQQ · L-lactate dehydrogenase a chain: “Rabbit muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate”. X-ray diffraction, 3 ligands (NAI, OAA, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #128455 on GenesisL1: 3D…
- PDB
- 5NQQ
- Type
- protein
- Length
- 1,324 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
- P13491
- Ligands
- NAI, OAA, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 46% helix, 19% strand | P13491 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- OAA · Oxaloacetate ion · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
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 | 1133 | 0.89 | 0.91 | 119 | SO4 |
| 2 | 236 | 0.72 | 0.87 | 41 | NAI, OAA |
| 3 | 258 | 0.70 | 0.85 | 41 | NAI |
| 4 | 75 | 0.67 | 0.94 | 15 | empty |
| 5 | 515 | 0.64 | 0.76 | 54 | NAI |
Interfaces
6 interfaces between chains.
- C–D · 2875 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2871 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1734 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1721 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 955 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5NQQ · Rabbit Muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate · the same entry in another collection · chain A against A, TM-score 1.00
- P13491 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P13491) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13491
- Elsewhere: RCSB PDB 5NQQ · PDBe 5NQQ · UniProt P13491
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