MolNFT v2 · #9587 · protein
Human heart L-lactate dehydrogenase H chain, ternary complex with NADH and oxamate
1I0Z: “Human heart L-lactate dehydrogenase H chain, ternary complex with NADH and oxamate”. X-ray diffraction at 2.1, 2 ligands (NAI, OXM), 9 pockets (best druggability 0.73). MolNFT v2 #9587 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1I0Z
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens
- Molecule
- L-lactate dehydrogenase H chain
- EC
- 1.1.1.27
- UniProt
- P07195
- Ligands
- NAI, OXM
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase H chain (EC 1.1.1.27) | protein | 332 | 45% helix, 17% strand | P07195 |
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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.73 | 0.86 | 57 | NAI, OXM |
| 2 | 266 | 0.71 | 0.85 | 41 | NAI, OXM |
| 3 | 210 | 0.56 | 0.79 | 37 | empty |
| 4 | 70 | 0.39 | 0.79 | 16 | empty |
| 5 | 72 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2738 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1I0Z · Human heart L-lactate dehydrogenase H chain, ternary complex with NADH and oxamate · the same entry in another collection · chain A against A, TM-score 1.00
- P07195 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase B chain (P07195) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07195
- Elsewhere: RCSB PDB 1I0Z · PDBe 1I0Z · UniProt P07195
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