Research workbench
Crystal structure of human IDH3 holoenzyme in apo form.
Analyse Crystal structure of human IDH3 holoenzyme in apo form. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CE3
- Type
- protein
- Length
- 1,338 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitrate dehydrogenase…
- EC
- 1.1.1.41
- UniProt
- P50213, P51553, O43837
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 326 | 40% helix, 17% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial | protein | 345 | 40% helix, 20% strand | P51553 |
| C | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 335 | 40% helix, 19% strand | P50213 |
| D | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 332 | 43% helix, 20% strand | O43837 |
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 23 | empty |
| 2 | 476 | 0.75 | 0.84 | 61 | empty |
| 3 | 62 | 0.75 | 0.99 | 20 | empty |
| 4 | 542 | 0.70 | 0.80 | 60 | empty |
| 5 | 99 | 0.69 | 0.92 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2199 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2063 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CE3 · Crystal structure of human IDH3 holoenzyme in APO form. · the same entry in another collection · chain D against D, TM-score 1.00
- P51553 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit gamma… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P50213 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- O43837 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit beta… · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P50213
- Every structure of UniProt P51553
- Every structure of UniProt O43837
- Elsewhere: RCSB PDB 7CE3 · PDBe 7CE3 · UniProt P50213 · UniProt P51553 · UniProt O43837
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