Research workbench
Acek (D477A) icdh complex
Analyse Acek (D477A) icdh complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P69
- 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
- Q8X607, P08200
- Ligands
- AMP, ADP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 554 | 44% helix, 16% strand | Q8X607 |
| B | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 561 | 44% helix, 16% strand | Q8X607 |
| C, D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 415 | 40% helix, 20% strand | P08200 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.86 | 0.87 | 111 | empty |
| 2 | 1015 | 0.85 | 0.85 | 95 | empty |
| 3 | 497 | 0.74 | 0.83 | 51 | AMP |
| 4 | 337 | 0.74 | 0.85 | 34 | AMP |
| 5 | 467 | 0.74 | 0.83 | 53 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3091 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1307 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 571 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide, 2 covalent (isopeptide, covalent ligand).
Compared structures
- 4P69 · Acek (D477A) ICDH complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X607 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase KINASE/PHOSPHATASE (Q8X607) · a predicted model of the same protein · chain B 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 Q8X607
- Every structure of UniProt P08200
- Elsewhere: RCSB PDB 4P69 · PDBe 4P69 · UniProt Q8X607 · UniProt P08200
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