Research workbench
Crystal structure of D-lactate dehydrogenase from aquifex aeolicus complexed with NAD and lactic acid
Analyse Crystal structure of D-lactate dehydrogenase from aquifex aeolicus complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KB6
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- O66939
- Ligands
- LAC, NAD
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 333 | 44% helix, 17% strand | O66939 |
| B, C, D | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 334 | 45% helix, 17% strand | O66939 |
Ligands and binding sites
- LAC · Lactic acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 8 copies · chains A, B, C
- PPI · Propanoic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.81 | 0.84 | 75 | PEG, GOL |
| 2 | 513 | 0.71 | 0.80 | 52 | PPI, GOL |
| 3 | 476 | 0.70 | 0.80 | 51 | PPI |
| 4 | 495 | 0.70 | 0.80 | 55 | PPI, GOL |
| 5 | 313 | 0.70 | 0.83 | 42 | LAC, NAD |
Interfaces
6 interfaces between chains.
- A–B · 2498 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2471 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 587 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 583 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3KB6 · Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and… · the same entry in another collection · chain A against A, TM-score 1.00
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 O66939
- Elsewhere: RCSB PDB 3KB6 · PDBe 3KB6 · UniProt O66939
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