Research workbench
D-lactate dehydrogenase complexed with NADH and oxamate
Analyse D-lactate dehydrogenase complexed with NADH and oxamate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DLD
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- P30901
- Ligands
- NAI, OXM
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 337 | 39% helix, 16% strand | P30901 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- OXM · Oxamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.74 | 0.77 | 64 | NAI, OXM |
| 2 | 612 | 0.64 | 0.74 | 52 | NAI, OXM |
| 3 | 243 | 0.57 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2929 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
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 P30901
- Elsewhere: RCSB PDB 2DLD · PDBe 2DLD · UniProt P30901
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