Research workbench
Crystal structure of the alpha beta heterodimer of human IDH3 in APO form.
Analyse Crystal structure of the alpha beta heterodimer of human IDH3 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
- 6KDF
- Type
- protein
- Length
- 5,218 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Homo sapiens
- Molecule
- Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitrate dehydrogenase…
- EC
- 1.1.1.41
- UniProt
- P50213, O43837
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.05 · 11 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 333 | 42% helix, 23% strand | P50213 |
| C, D, H | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 319 | 43% helix, 23% strand | O43837 |
| A, G, M, O | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 335 | 45% helix, 23% strand | P50213 |
| E | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 338 | 44% helix, 22% strand | P50213 |
| F | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 315 | 45% helix, 23% strand | O43837 |
| I | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 333 | 42% helix, 21% strand | P50213 |
| J | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 316 | 45% helix, 23% strand | O43837 |
| K | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 333 | 42% helix, 20% strand | P50213 |
| L | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 317 | 44% helix, 23% strand | O43837 |
| N | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 316 | 43% helix, 24% strand | O43837 |
| P | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 320 | 42% helix, 23% strand | O43837 |
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 | 1037 | 0.81 | 0.82 | 100 | empty |
| 2 | 998 | 0.79 | 0.80 | 103 | empty |
| 3 | 545 | 0.77 | 0.83 | 64 | empty |
| 4 | 1129 | 0.74 | 0.77 | 108 | empty |
| 5 | 571 | 0.73 | 0.81 | 51 | empty |
Interfaces
32 interfaces between chains.
- A–D · 2185 Ų buried · 33 hydrogen bonds · protein-protein
- K–L · 2158 Ų buried · 35 hydrogen bonds · protein-protein
- O–P · 2136 Ų buried · 33 hydrogen bonds · protein-protein
- M–N · 2135 Ų buried · 29 hydrogen bonds · protein-protein
- I–J · 2134 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6KDF · Crystal structure of the alpha beta heterodimer of human IDH3 in apo form. · the same entry in another collection · chain J against J, 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 P50213
- Every structure of UniProt O43837
- Elsewhere: RCSB PDB 6KDF · PDBe 6KDF · UniProt P50213 · UniProt O43837
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