MolNFT v1 · #18771 · protein
T.GONDII LDH1 complexed with apad and sulfate at 1.6 ångströms
1PZG · Lactate dehydrogenase: “T.GONDII LDH1 complexed with apad and sulfate at 1.6 ångströms”. X-ray diffraction, 2 ligands (A3D, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #18771 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1PZG
- Type
- protein
- Length
- 1,307 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
- A3D, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 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 | Lactate dehydrogenase (EC 1.1.1.27) | protein | 325 | 51% helix, 19% strand | P90613 |
| D | Lactate dehydrogenase (EC 1.1.1.27) | protein | 326 | 50% helix, 19% strand | P90613 |
Ligands and binding sites
- A3D · 3-acetylpyridine adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.83 | 0.84 | 100 | empty |
| 2 | 673 | 0.77 | 0.82 | 87 | SO4, A3D |
| 3 | 431 | 0.69 | 0.80 | 54 | SO4, A3D |
| 4 | 256 | 0.69 | 0.84 | 42 | SO4, A3D |
| 5 | 207 | 0.45 | 0.74 | 35 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2123 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2115 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1483 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1474 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 1PZG · T.gondii LDH1 complexed with APAD and sulfate at 1.6 Angstroms · 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 1PZG · PDBe 1PZG · UniProt P90613
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