Research workbench
T.GONDII LDH1 ternary complex with apad+ and oxalate
Analyse T.GONDII LDH1 ternary complex with apad+ and oxalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PZF
- Type
- protein
- Length
- 1,308 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
- OXL, A3D
- Pockets
- 17 · 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 | 328 | 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
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- A3D · 3-acetylpyridine adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.82 | 0.84 | 99 | empty |
| 2 | 715 | 0.76 | 0.81 | 91 | OXL, A3D |
| 3 | 636 | 0.76 | 0.82 | 89 | OXL, A3D |
| 4 | 119 | 0.45 | 0.78 | 24 | empty |
| 5 | 78 | 0.45 | 0.81 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2144 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2113 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1483 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1470 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1PZF · T.gondii LDH1 ternary complex with APAD+ and oxalate · 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 1PZF · PDBe 1PZF · UniProt P90613
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