Research workbench
L-lactate dehydrogenase from thermus caldophilus GK24 complexed with oxamate, NADH and fbp
Analyse L-lactate dehydrogenase from thermus caldophilus GK24 complexed with oxamate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VPH
- Type
- protein
- Length
- 1,240 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
- P06150
- Ligands
- OXM, NAD, FBP
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 49% helix, 21% strand | P06150 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.85 | 0.90 | 69 | FBP, GOL |
| 2 | 378 | 0.82 | 0.91 | 48 | FBP, GOL |
| 3 | 187 | 0.72 | 0.89 | 24 | empty |
| 4 | 694 | 0.71 | 0.78 | 58 | OXM, NAD |
| 5 | 550 | 0.66 | 0.77 | 49 | OXM, NAD |
Interfaces
6 interfaces between chains.
- C–D · 2257 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2212 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1055 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1017 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3VPH · L-lactate dehydrogenase from Thermus caldophilus GK24 complexed with oxamate, NADH and FBP · the same entry in another collection · chain A against A, TM-score 1.00
- P06150 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P06150) · 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 P06150
- Elsewhere: RCSB PDB 3VPH · PDBe 3VPH · UniProt P06150
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