MolNFT v1 · #117036 · protein
Crystal structure of 2'AMP bound saimpase-II
5DW8 · Inositol monophosphatase: “Crystal structure of 2'AMP bound saimpase-II”. X-ray diffraction, 2 ligands (2AM, CA), 7 pockets (best druggability 0.71). MolNFT v1 #117036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DW8
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- EC
- 3.1.3.25
- UniProt
- A0A0C5I0W4
- Ligands
- 2AM, CA
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase (EC 3.1.3.25) | protein | 260 | 45% helix, 25% strand | A0A0C5I0W4 |
| B | Inositol monophosphatase (EC 3.1.3.25) | protein | 259 | 45% helix, 24% strand | A0A0C5I0W4 |
Ligands and binding sites
- 2AM · Adenosine-2'-monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 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 | 607 | 0.71 | 0.79 | 63 | empty |
| 2 | 252 | 0.58 | 0.79 | 32 | 2AM, CA, GOL |
| 3 | 235 | 0.56 | 0.79 | 32 | 2AM |
| 4 | 62 | 0.45 | 0.83 | 16 | empty |
| 5 | 91 | 0.39 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1304 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5DW8 · Crystal structure of 2'AMP bound SaIMPase-II · the same entry in another collection · chain A 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 A0A0C5I0W4
- Elsewhere: RCSB PDB 5DW8 · PDBe 5DW8 · UniProt A0A0C5I0W4
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