Research workbench
Crystal structure of L-lactate dehydrogenase from bacillus subtilis complexed with fbp and NAD+
Analyse Crystal structure of L-lactate dehydrogenase from bacillus subtilis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PQD
- Type
- protein
- Length
- 2,449 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P13714
- Ligands
- FBP, NAD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 47% helix, 18% strand | P13714 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 312 | 47% helix, 21% strand | P13714 |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 301 | 50% helix, 20% strand | P13714 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 301 | 48% helix, 18% strand | P13714 |
| E, F | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 311 | 48% helix, 20% strand | P13714 |
| G | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 302 | 48% helix, 18% strand | P13714 |
| H | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 301 | 48% helix, 21% strand | P13714 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, C, B, D, F, G, H, E
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.89 | 0.93 | 131 | FBP |
| 2 | 483 | 0.85 | 0.92 | 78 | FBP |
| 3 | 269 | 0.80 | 0.93 | 47 | FBP |
| 4 | 541 | 0.77 | 0.84 | 45 | empty |
| 5 | 509 | 0.73 | 0.82 | 49 | empty |
Interfaces
15 interfaces between chains.
- B–C · 2320 Ų buried · 23 hydrogen bonds · protein-protein
- E–H · 2292 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2286 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 2261 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 893 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3PQD · Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP… · the same entry in another collection · chain H against H, TM-score 1.00
- P13714 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P13714) · a predicted model of the same protein · chain H 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 P13714
- Elsewhere: RCSB PDB 3PQD · PDBe 3PQD · UniProt P13714
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