Research workbench
Rabbit muscle L-lactate dehydrogenase in complex with malonate
Analyse Rabbit muscle L-lactate dehydrogenase in complex with malonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQB
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P13491
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 18% strand | P13491 |
Ligands and binding sites
- MLI · Malonate ion · additive · 7 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.89 | 0.91 | 118 | MLI |
| 2 | 94 | 0.70 | 0.94 | 17 | empty |
| 3 | 491 | 0.68 | 0.79 | 55 | MLI |
| 4 | 68 | 0.68 | 0.95 | 21 | MLI |
| 5 | 70 | 0.67 | 0.94 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2926 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2919 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1672 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1655 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 953 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NQB · Rabbit Muscle L-lactate dehydrogenase in complex with malonate · the same entry in another collection · chain C against C, TM-score 1.00
- P13491 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P13491) · 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 P13491
- Elsewhere: RCSB PDB 5NQB · PDBe 5NQB · UniProt P13491
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