Research workbench
Structure of salmonella D-lactate dehydrogenase in complex with NADH
Analyse Structure of salmonella D-lactate dehydrogenase in complex with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CUK
- Type
- protein
- Length
- 1,330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- Q8Z780
- Ligands
- NAI
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 330 | 40% helix, 18% strand | Q8Z780 |
| B, C | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 335 | 40% helix, 17% strand | Q8Z780 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.69 | 0.77 | 85 | empty |
| 2 | 427 | 0.69 | 0.81 | 54 | empty |
| 3 | 425 | 0.65 | 0.78 | 45 | empty |
| 4 | 414 | 0.64 | 0.78 | 57 | empty |
| 5 | 363 | 0.63 | 0.78 | 43 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2692 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2691 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 574 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 549 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4CUK · Structure of Salmonella D-Lactate Dehydrogenase in 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
- Every structure of UniProt Q8Z780
- Elsewhere: RCSB PDB 4CUK · PDBe 4CUK · UniProt Q8Z780
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.