Research workbench
Crystal structure of IMPASE/NADP phosphatase complexed with NADP and CA2+
Analyse Crystal structure of IMPASE/NADP phosphatase complexed with NADP and CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYG
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- EC
- 3.1.3.25
- UniProt
- A0A0D6HL44
- Ligands
- NAP, CA, CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase (EC 3.1.3.25) | protein | 256 | 40% helix, 23% strand | A0A0D6HL44 |
| B | Inositol monophosphatase (EC 3.1.3.25) | protein | 265 | 42% helix, 23% strand | A0A0D6HL44 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PGE · Triethylene glycol · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.65 | 0.94 | 21 | PG0, CL |
| 2 | 256 | 0.55 | 0.77 | 29 | CA, NAP |
| 3 | 321 | 0.54 | 0.75 | 40 | PGE, GOL |
| 4 | 223 | 0.53 | 0.77 | 33 | CA, NAP |
| 5 | 192 | 0.44 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1406 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5EYG · Crystal structure of IMPase/NADP phosphatase complexed with NADP and Ca2+ · 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 A0A0D6HL44
- Elsewhere: RCSB PDB 5EYG · PDBe 5EYG · UniProt A0A0D6HL44
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