Research workbench
Sus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate
Analyse Sus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CEP
- Type
- protein
- Length
- 1,301 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase B chain
- EC
- 1.1.1.27
- UniProt
- P00336
- Ligands
- NAD, OXM
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase B chain (EC 1.1.1.27) | protein | 331 | 46% helix, 18% strand | P00336 |
| B | L-lactate dehydrogenase B chain (EC 1.1.1.27) | protein | 322 | 45% helix, 19% strand | P00336 |
| D | L-lactate dehydrogenase B chain (EC 1.1.1.27) | protein | 317 | 46% helix, 20% strand | P00336 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.87 | 0.88 | 126 | empty |
| 2 | 1122 | 0.74 | 0.77 | 110 | empty |
| 3 | 257 | 0.71 | 0.86 | 42 | NAD, OXM |
| 4 | 117 | 0.70 | 0.92 | 19 | empty |
| 5 | 122 | 0.69 | 0.91 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2683 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2661 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1499 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1492 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 967 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6CEP · Sus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate · the same entry in another collection · chain A against A, TM-score 1.00
- P00336 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase B chain (P00336) · a predicted model of the same protein · chain B 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 P00336
- Elsewhere: RCSB PDB 6CEP · PDBe 6CEP · UniProt P00336
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