MolNFT v1 · #153697 · protein
Re-refined structure of R-state L-lactate dehydrogenase fromlactobacillus casei
6JML: “Re-refined structure of R-state L-lactate dehydrogenase fromlactobacillus casei”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #153697 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6JML
- Type
- protein
- Length
- 1,853 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
- P00343
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 309 | 52% helix, 20% strand | P00343 |
| B, F | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 51% helix, 20% strand | P00343 |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 296 | 51% helix, 21% strand | P00343 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 304 | 51% helix, 21% strand | P00343 |
| E | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 314 | 51% helix, 20% strand | P00343 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.84 | 0.89 | 89 | SO4 |
| 2 | 445 | 0.82 | 0.89 | 64 | SO4 |
| 3 | 379 | 0.65 | 0.79 | 45 | SO4 |
| 4 | 363 | 0.62 | 0.78 | 40 | SO4 |
| 5 | 354 | 0.59 | 0.77 | 39 | SO4 |
Interfaces
7 interfaces between chains.
- D–F · 1962 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 1956 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1940 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1123 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1110 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6JML · Re-refined structure of R-state L-lactate dehydrogenase fromLactobacillus casei · the same entry in another collection · chain F against F, TM-score 1.00
- P00343 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P00343) · a predicted model of the same protein · chain C 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 P00343
- Elsewhere: RCSB PDB 6JML · PDBe 6JML · UniProt P00343
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