Research workbench
Crystal structure of isocitrate dehydrogenase from Methylococcus capsulatus
Analyse Crystal structure of isocitrate dehydrogenase from Methylococcus capsulatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKY
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
- Molecule
- Putative isocitrate dehydrogenase, NAD-dependent
- UniProt
- Q602J2
- Ligands
- ACE, NAD
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative isocitrate dehydrogenase, NAD-dependent | protein | 339 | 42% helix, 22% strand | Q602J2 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.75 | 0.82 | 50 | NAD, CIT |
| 2 | 502 | 0.73 | 0.82 | 47 | NAD, ACE, CIT |
| 3 | 238 | 0.62 | 0.81 | 28 | empty |
| 4 | 225 | 0.60 | 0.80 | 28 | empty |
| 5 | 144 | 0.58 | 0.83 | 26 | ACE |
Interfaces
1 interface between chains.
- A–B · 2524 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 6LKY · Crystal structure of isocitrate dehydrogenase from methylococcus capsulatus · 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 Q602J2
- Elsewhere: RCSB PDB 6LKY · PDBe 6LKY · UniProt Q602J2
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