Research workbench
Crystal structure of predicted metal-dependent phosphohydrolase (ZP_00055740.2) from magnetospirillum magnetotacticum ms-1 at 1.37 a resolution
Analyse Crystal structure of predicted metal-dependent phosphohydrolase (ZP_00055740.2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KH1
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted metal-dependent phosphohydrolase
- UniProt
- D1MPT5
- Ligands
- CA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted metal-dependent phosphohydrolase | protein | 196 | 67% helix, 5% strand | D1MPT5 |
| B | Predicted metal-dependent phosphohydrolase | protein | 189 | 68% helix, 5% strand | D1MPT5 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.72 | 0.89 | 32 | CA |
| 2 | 176 | 0.71 | 0.89 | 34 | empty |
| 3 | 140 | 0.42 | 0.75 | 20 | PG4 |
Interfaces
1 interface between chains.
- A–B · 2170 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3KH1 · Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from… · 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 D1MPT5
- Elsewhere: RCSB PDB 3KH1 · PDBe 3KH1 · UniProt D1MPT5 · AlphaFold DB D1MPT5
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