MolNFT v1 · #154508 · protein
Crystal structure of the alpha beta heterodimer of human IDH3 in apo form.
6KDF · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha beta heterodimer of human IDH3 in apo form.”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #154508 on GenesisL1: 3D…
- PDB
- 6KDF
- Type
- protein
- Length
- 5,218 residues
- Chains
- 16
- 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, O43837
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 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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