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The structure of wt a. thaliana IGPD2 in complex with MN2+ and phosphate
Analyse The structure of wt a. thaliana IGPD2 in complex with MN2+ and phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QNK
- Type
- protein
- Length
- 1,479 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
- EC
- 4.2.1.19
- UniProt
- O23346
- Ligands
- MN, NA, PO4
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic (EC 4.2.1.19) | protein | 185 | 36% helix, 33% strand | O23346 |
| F | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic (EC 4.2.1.19) | protein | 184 | 36% helix, 33% strand | O23346 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 16 copies · chains A, D, B, C, E, H, F, G
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.64 | 0.80 | 45 | empty |
| 2 | 268 | 0.59 | 0.79 | 26 | empty |
| 3 | 165 | 0.49 | 0.77 | 19 | empty |
| 4 | 158 | 0.49 | 0.78 | 22 | empty |
| 5 | 184 | 0.48 | 0.76 | 21 | empty |
Interfaces
8 interfaces between chains.
- E–F · 608 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 607 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 606 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 600 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4QNK · The structure of wt A. thaliana IGPD2 in complex with Mn2+ and phosphate · the same entry in another collection · chain H against H, TM-score 1.00
- O23346 · AlphaFold monomer V2.0 prediction for imidazoleglycerol-phosphate dehydratase 2… · a predicted model of the same protein · chain F against A, 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 O23346
- Elsewhere: RCSB PDB 4QNK · PDBe 4QNK · UniProt O23346
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