Research workbench
Crystal structure of L-lactate dehydrogenase from bacillus subtilis with H171C mutation
Analyse Crystal structure of L-lactate dehydrogenase from bacillus subtilis with H171C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PQE
- Type
- protein
- Length
- 1,239 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% 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 | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 48% helix, 19% strand | P13714 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 306 | 48% helix, 19% strand | P13714 |
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 | 728 | 0.81 | 0.85 | 82 | empty |
| 2 | 592 | 0.81 | 0.86 | 75 | empty |
| 3 | 443 | 0.66 | 0.79 | 48 | empty |
| 4 | 425 | 0.65 | 0.78 | 53 | empty |
| 5 | 402 | 0.63 | 0.78 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2063 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2043 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 805 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3PQE · Crystal structure of L-lactate dehydrogenase from Bacillus subtilis with H171C mutation · 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 3PQE · PDBe 3PQE · UniProt P13714
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