Research workbench
Crystal structure of medicago truncatula histidinol-phosphate phosphatase (mthpp) in complex with L-histidinol phosphate and MG2+
Analyse Crystal structure of medicago truncatula histidinol-phosphate phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQ9
- Type
- protein
- Length
- 1,026 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- UniProt
- G7J7Q5
- Ligands
- HSA, MG
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase | protein | 254 | 35% helix, 26% strand | G7J7Q5 |
| B | Inositol monophosphatase | protein | 260 | 35% helix, 26% strand | G7J7Q5 |
| C | Inositol monophosphatase | protein | 258 | 34% helix, 26% strand | G7J7Q5 |
| D | Inositol monophosphatase | protein | 254 | 35% helix, 26% strand | G7J7Q5 |
Ligands and binding sites
- HSA · Phosphoric acid mono-[2-amino-3-(3H-imidazol-4-yl)-propyl]ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.78 | 0.80 | 100 | HSA |
| 2 | 189 | 0.60 | 0.82 | 37 | HSA |
| 3 | 245 | 0.58 | 0.79 | 41 | HSA |
| 4 | 444 | 0.57 | 0.73 | 45 | empty |
| 5 | 189 | 0.55 | 0.79 | 34 | HSA |
Interfaces
5 interfaces between chains.
- A–B · 1351 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1171 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 449 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EQ9 · Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in… · the same entry in another collection · chain C against C, 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 G7J7Q5
- Elsewhere: RCSB PDB 5EQ9 · PDBe 5EQ9 · UniProt G7J7Q5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.