MolNFT v1 · #153297 · protein
Complex structure of lactobacillus casei lactate dehydrogenase penta mutant with pyruvate
6J9U · L-lactate dehydrogenase: “Complex structure of lactobacillus casei lactate dehydrogenase penta mutant with pyruvate”. X-ray diffraction, 2 ligands (PYR, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #153297 on GenesisL1: 3D…
- PDB
- 6J9U
- Type
- protein
- Length
- 1,882 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- S6C1Z0
- Ligands
- PYR, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 306 | 49% helix, 21% strand | S6C1Z0 |
| B, C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 50% helix, 20% strand | S6C1Z0 |
| E | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 50% helix, 20% strand | S6C1Z0 |
| F | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 49% helix, 20% strand | S6C1Z0 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, F, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.83 | 0.88 | 81 | SO4 |
| 2 | 471 | 0.82 | 0.89 | 65 | SO4 |
| 3 | 1041 | 0.77 | 0.79 | 83 | SO4 |
| 4 | 813 | 0.75 | 0.79 | 80 | PYR |
| 5 | 272 | 0.69 | 0.84 | 45 | PYR |
Interfaces
9 interfaces between chains.
- A–B · 2118 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 2100 Ų buried · 35 hydrogen bonds · protein-protein
- C–E · 2096 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1158 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1114 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6J9U · Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate · 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 S6C1Z0
- Elsewhere: RCSB PDB 6J9U · PDBe 6J9U · UniProt S6C1Z0
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