Research workbench
Crystal structure of L-lactate dehydrogenase from bacillus subtilis mutation H171C complexed with NAD+
Analyse Crystal structure of L-lactate dehydrogenase from bacillus subtilis mutation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PQF
- Type
- protein
- Length
- 1,252 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P13714
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 314 | 49% helix, 19% strand | P13714 |
| C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 312 | 47% helix, 19% strand | P13714 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains C, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.81 | 0.86 | 77 | empty |
| 2 | 669 | 0.80 | 0.85 | 79 | empty |
| 3 | 432 | 0.65 | 0.78 | 45 | empty |
| 4 | 423 | 0.65 | 0.78 | 50 | empty |
| 5 | 571 | 0.64 | 0.75 | 62 | NAD |
Interfaces
6 interfaces between chains.
- B–C · 1998 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1993 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 837 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 823 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3PQF · Crystal structure of L-lactate dehydrogenase from Bacillus subtilis mutation H171C… · the same entry in another collection · chain A against A, TM-score 1.00
- P13714 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P13714) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3PQF · PDBe 3PQF · UniProt P13714
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