Research workbench
Yeast isocitrate dehydrogenase (apo form)
Analyse Yeast isocitrate dehydrogenase (apo form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BLX
- Type
- protein
- Length
- 5,431 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NAD] subunit 1; Isocitrate dehydrogenase [NAD] subunit 2
- EC
- 1.1.1.41
- UniProt
- P28834, P28241
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 335 | 47% helix, 22% strand | P28834 |
| B, L | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 346 | 41% helix, 22% strand | P28241 |
| C, K | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 338 | 46% helix, 24% strand | P28834 |
| D, F, H, J, N | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 345 | 40% helix, 22% strand | P28241 |
| E | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 341 | 46% helix, 22% strand | P28834 |
| G | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 334 | 46% helix, 23% strand | P28834 |
| I | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 333 | 47% helix, 23% strand | P28834 |
| M | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 337 | 46% helix, 23% strand | P28834 |
| O | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 332 | 47% helix, 23% strand | P28834 |
| P | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 326 | 42% helix, 22% strand | P28241 |
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 | 643 | 0.75 | 0.82 | 61 | empty |
| 2 | 74 | 0.74 | 0.98 | 25 | empty |
| 3 | 82 | 0.74 | 0.97 | 20 | empty |
| 4 | 85 | 0.74 | 0.96 | 21 | empty |
| 5 | 74 | 0.73 | 0.97 | 21 | empty |
Interfaces
34 interfaces between chains.
- E–F · 2183 Ų buried · 22 hydrogen bonds · protein-protein
- M–N · 2179 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2152 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 2149 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 2147 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BLX · Yeast Isocitrate Dehydrogenase (Apo Form) · the same entry in another collection · chain K against K, 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 P28834
- Every structure of UniProt P28241
- Elsewhere: RCSB PDB 3BLX · PDBe 3BLX · UniProt P28834 · UniProt P28241
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