MolNFT v1 · #102369 · protein
Crystal structure of human muscle L-lactate dehydrogenase
4OJN · L-lactate dehydrogenase a chain: “Crystal structure of human muscle L-lactate dehydrogenase”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #102369 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OJN
- Type
- protein
- Length
- 2,651 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 332 | 45% helix, 19% strand | P00338 |
| B, E, F, G, H | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 44% helix, 18% strand | P00338 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.89 | 0.91 | 130 | GOL |
| 2 | 1054 | 0.89 | 0.91 | 114 | empty |
| 3 | 589 | 0.67 | 0.77 | 59 | 1PE |
| 4 | 58 | 0.67 | 0.95 | 15 | empty |
| 5 | 555 | 0.67 | 0.77 | 62 | 1PE |
Interfaces
14 interfaces between chains.
- G–H · 2882 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2882 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2869 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2858 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1769 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4OJN · Crystal structure of human muscle L-lactate dehydrogenase · 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 P00338
- Elsewhere: RCSB PDB 4OJN · PDBe 4OJN · UniProt P00338
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