Research workbench
Trichomonas vaginalis lactate dehydrogenase in complex with NADH and oxamate
Analyse Trichomonas vaginalis lactate dehydrogenase in complex 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
- 5A1T
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- O96445
- Ligands
- NAI, OXM
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 331 | 47% helix, 20% strand | O96445 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 328 | 46% helix, 20% strand | O96445 |
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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.75 | 0.78 | 84 | empty |
| 2 | 452 | 0.72 | 0.82 | 50 | NAI, OXM |
| 3 | 437 | 0.72 | 0.82 | 50 | NAI, OXM |
| 4 | 145 | 0.43 | 0.75 | 27 | empty |
| 5 | 113 | 0.43 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5A1T · Trichomonas vaginalis lactate dehydrogenase in complex with NADH and oxamate · 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 O96445
- Elsewhere: RCSB PDB 5A1T · PDBe 5A1T · UniProt O96445
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