Research workbench
T. gondii bradyzoite-specific ldh (LDH1) in complex with NAD and oxq
Analyse T. gondii bradyzoite-specific ldh (LDH1) in complex with NAD and oxq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OM9
- Type
- protein
- Length
- 1,310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P90613
- Ligands
- NAD, OXQ
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactate dehydrogenase (EC 1.1.1.27) | protein | 329 | 50% helix, 19% strand | P90613 |
| C, D | Lactate dehydrogenase (EC 1.1.1.27) | protein | 326 | 50% helix, 19% strand | P90613 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- OXQ · 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid · ligand · 4 copies · chains A, B, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.82 | 0.84 | 101 | empty |
| 2 | 686 | 0.77 | 0.82 | 90 | NAD, OXQ |
| 3 | 736 | 0.77 | 0.82 | 91 | NAD, OXQ |
| 4 | 154 | 0.45 | 0.76 | 25 | empty |
| 5 | 171 | 0.43 | 0.74 | 33 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2112 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2096 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 1496 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1465 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3OM9 · T. Gondii bradyzoite-specific LDH (LDH1) in complex with NAD and OXQ · 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 P90613
- Elsewhere: RCSB PDB 3OM9 · PDBe 3OM9 · UniProt P90613
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