MolNFT v1 · #98887 · protein
Crystal structure of L-lactate dehydrogenase from bacillus cereus atcc 14579 complexed with calcium, nysgrc target 029452
4LN1 · L-lactate dehydrogenase 1: “Crystal structure of L-lactate dehydrogenase from bacillus cereus atcc 14579 complexed with calcium, nysgrc…”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.87). MolNFT v1 #98887 on…
- PDB
- 4LN1
- Type
- protein
- Length
- 1,269 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase 1
- EC
- 1.1.1.27
- UniProt
- Q81EP4
- Ligands
- CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 317 | 50% helix, 20% strand | Q81EP4 |
| B | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 321 | 51% helix, 20% strand | Q81EP4 |
| C | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 316 | 51% helix, 19% strand | Q81EP4 |
| D | L-lactate dehydrogenase 1 (EC 1.1.1.27) | protein | 315 | 51% helix, 19% strand | Q81EP4 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C, B, D
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 | 1038 | 0.87 | 0.88 | 93 | CA |
| 2 | 482 | 0.82 | 0.89 | 48 | empty |
| 3 | 540 | 0.67 | 0.77 | 50 | empty |
| 4 | 477 | 0.64 | 0.77 | 44 | empty |
| 5 | 325 | 0.62 | 0.79 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2236 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2232 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1198 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1196 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 898 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4LN1 · CRYSTAL STRUCTURE OF L-lactate dehydrogenase from Bacillus cereus ATCC 14579 complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- Q81EP4 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase 1 (Q81EP4) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q81EP4
- Elsewhere: RCSB PDB 4LN1 · PDBe 4LN1 · UniProt Q81EP4
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