Research workbench
The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE in complex with its substrate, isocitrate dehydrogenase, from escherichia COLI.
Analyse The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCB
- Type
- protein
- Length
- 1,945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase KINASE/PHOSPHATASE; Isocitrate dehydrogenase [NADP]
- EC
- 2.7.11.5, 3.1.3.-, 1.1.1.42
- UniProt
- B5Z0A8, P08200
- Ligands
- AMP, ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 554 | 46% helix, 18% strand | B5Z0A8 |
| B | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 561 | 44% helix, 17% strand | B5Z0A8 |
| C, D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 415 | 41% helix, 20% strand | P08200 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.86 | 0.88 | 117 | empty |
| 2 | 904 | 0.85 | 0.86 | 89 | empty |
| 3 | 321 | 0.82 | 0.91 | 55 | ATP, MG |
| 4 | 187 | 0.76 | 0.92 | 36 | ATP, MG |
| 5 | 447 | 0.76 | 0.84 | 56 | AMP |
Interfaces
4 interfaces between chains.
- C–D · 3143 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1384 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3LCB · The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its… · the same entry in another collection · chain A against A, TM-score 1.00
- B5Z0A8 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase KINASE/PHOSPHATASE (B5Z0A8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P08200 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P08200) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 B5Z0A8
- Every structure of UniProt P08200
- Elsewhere: RCSB PDB 3LCB · PDBe 3LCB · UniProt B5Z0A8 · UniProt P08200
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