Research workbench
Structural studies of metal binding by inositol monophosphatase: evidence for two-metal ion catalysis
Analyse Structural studies of metal binding by inositol monophosphatase: evidence for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IMD
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- EC
- 3.1.3.25
- UniProt
- P29218
- Ligands
- MN, PO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase (EC 3.1.3.25) | protein | 266 | 38% helix, 25% strand | P29218 |
| B | Inositol monophosphatase (EC 3.1.3.25) | protein | 272 | 37% helix, 25% strand | P29218 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.77 | 0.86 | 58 | MN, PO4 |
| 2 | 385 | 0.76 | 0.87 | 46 | MN, PO4 |
| 3 | 442 | 0.60 | 0.75 | 44 | empty |
| 4 | 114 | 0.44 | 0.77 | 16 | empty |
| 5 | 81 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1676 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1IMD · Structural studies of metal binding by inositol monophosphatase: evidence for two-metal… · the same entry in another collection · chain A against A, TM-score 1.00
- P29218 · AlphaFold monomer V2.0 prediction for inositol monophosphatase 1 (P29218) · a predicted model of the same protein · chain B 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 P29218
- Elsewhere: RCSB PDB 1IMD · PDBe 1IMD · UniProt P29218
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