Research workbench
X-ray structure of imidazoleglycerol-phosphate dehydratase
Analyse X-ray structure of imidazoleglycerol-phosphate dehydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F1D
- Type
- protein
- Length
- 2,928 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazoleglycerol-phosphate dehydratase 1
- EC
- 4.2.1.19
- UniProt
- P34047
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Imidazoleglycerol-phosphate dehydratase 1 (EC 4.2.1.19) | protein | 183 | 36% helix, 32% strand | P34047 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 32 copies · chains A, B, G, C, D, E, F, H, I, J, O, K, L, M, N, P
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.74 | 0.79 | 93 | SO4 |
| 2 | 654 | 0.71 | 0.78 | 35 | empty |
| 3 | 514 | 0.71 | 0.80 | 56 | empty |
| 4 | 645 | 0.70 | 0.78 | 35 | empty |
| 5 | 610 | 0.69 | 0.78 | 79 | SO4 |
Interfaces
26 interfaces between chains.
- N–O · 688 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 6 hydrogen bonds · protein-protein
- N–P · 682 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 669 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 669 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2F1D · X-Ray Structure of imidazoleglycerol-phosphate dehydratase · the same entry in another collection · chain P against P, 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 P34047
- Elsewhere: RCSB PDB 2F1D · PDBe 2F1D · UniProt P34047
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