MolNFT v1 · #59048 · protein
Yeast isocitrate dehydrogenase with citrate bound in the regulatory subunits
3BLV · Isocitrate dehydrogenase [NAD] subunit 1: “Yeast isocitrate dehydrogenase with citrate bound in the regulatory subunits”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #59048 on GenesisL1: 3D structure, binding…
- PDB
- 3BLV
- Type
- protein
- Length
- 2,737 residues
- Chains
- 8
- 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 0.72
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 331 | 40% helix, 23% strand | P28834 |
| B | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 345 | 40% helix, 20% strand | P28241 |
| C, E | Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41) | protein | 344 | 39% helix, 22% strand | P28834 |
| D, F | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 347 | 39% helix, 19% strand | P28241 |
| H | Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41) | protein | 348 | 39% helix, 19% strand | P28241 |
Ligands and binding sites
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D, E, F, G, H
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 | 451 | 0.72 | 0.82 | 52 | FLC |
| 2 | 476 | 0.72 | 0.82 | 56 | FLC |
| 3 | 473 | 0.72 | 0.82 | 55 | FLC |
| 4 | 429 | 0.72 | 0.82 | 54 | FLC |
| 5 | 306 | 0.70 | 0.83 | 41 | empty |
Interfaces
19 interfaces between chains.
- C–D · 2295 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2279 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2270 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 2259 Ų buried · 30 hydrogen bonds · protein-protein
- C–G · 1043 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3BLV · Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits · the same entry in another collection · chain H against H, TM-score 1.00
- P28834 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P28241 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit 2… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 3BLV · PDBe 3BLV · UniProt P28834 · UniProt P28241
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