Research workbench
Crystal structure of the monomeric isocitrate dehydrogenase in complex with NADP+
Analyse Crystal structure of the monomeric isocitrate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J1W
- Type
- protein
- Length
- 2,952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P16100
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 738 | 46% helix, 16% strand | P16100 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
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 | 1111 | 0.81 | 0.82 | 80 | NAP |
| 2 | 1115 | 0.81 | 0.82 | 82 | NAP |
| 3 | 1065 | 0.80 | 0.82 | 81 | NAP |
| 4 | 108 | 0.80 | 0.99 | 24 | empty |
| 5 | 1092 | 0.80 | 0.82 | 82 | NAP |
Interfaces
4 interfaces between chains.
- A–C · 320 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 288 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 256 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1J1W · Crystal Structure Of The Monomeric Isocitrate Dehydrogenase In Complex With NADP+ · the same entry in another collection · chain C against C, TM-score 1.00
- P16100 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P16100) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P16100
- Elsewhere: RCSB PDB 1J1W · PDBe 1J1W · UniProt P16100
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