MolNFT v1 · #126416 · protein
Apo structure of pseudomonas aeruginosa isocitrate dehydrogenase, icd.
5M2E · Isocitrate dehydrogenase [NADP]: “Apo structure of pseudomonas aeruginosa isocitrate dehydrogenase, icd.”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1 #126416 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5M2E
- Type
- protein
- Length
- 1,672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- Q02NB5
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 418 | 42% helix, 20% strand | Q02NB5 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.79 | 0.83 | 94 | empty |
| 2 | 1103 | 0.79 | 0.80 | 123 | empty |
| 3 | 950 | 0.77 | 0.80 | 104 | empty |
| 4 | 973 | 0.71 | 0.76 | 89 | empty |
| 5 | 110 | 0.65 | 0.89 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3249 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3168 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5M2E · Apo structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, ICD. · the same entry in another collection · chain A against A, TM-score 1.00
- Q02NB5 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (Q02NB5) · a predicted model of the same protein · chain A 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 Q02NB5
- Elsewhere: RCSB PDB 5M2E · PDBe 5M2E · UniProt Q02NB5
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