MolNFT v1 · #18772 · protein
T.GONDII LDH1 ternary complex with NAD and oxalate
1PZH · Lactate dehydrogenase: “T.GONDII LDH1 ternary complex with NAD and oxalate”. X-ray diffraction, 2 ligands (OXL, NAD), 18 pockets (best druggability 0.83). MolNFT v1 #18772 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1PZH
- 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
- OXL, NAD
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactate dehydrogenase (EC 1.1.1.27) | protein | 329 | 50% helix, 18% strand | P90613 |
| C, D | Lactate dehydrogenase (EC 1.1.1.27) | protein | 326 | 50% helix, 18% strand | P90613 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-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
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.83 | 0.84 | 103 | empty |
| 2 | 709 | 0.76 | 0.81 | 91 | OXL, NAD |
| 3 | 393 | 0.68 | 0.81 | 47 | OXL, NAD |
| 4 | 254 | 0.67 | 0.84 | 43 | OXL, NAD |
| 5 | 83 | 0.49 | 0.83 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2127 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2122 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1479 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1475 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1080 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1PZH · T.gondii LDH1 ternary complex with NAD and oxalate · the same entry in another collection · chain B against B, 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 1PZH · PDBe 1PZH · UniProt P90613
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