Research workbench
The 3-dimensional structure of the gadolinium derivative of mpgp, the mannosyl-3-phosphoglycerate phosphatase from thermus thermophilus HB27
Analyse The 3-dimensional structure of the gadolinium derivative of mpgp, the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZTY
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.70
- UniProt
- Q72K29
- Ligands
- GD, CL
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 251 | 39% helix, 20% strand | Q72K29 |
Ligands and binding sites
- GD · Gadolinium atom · metal · 6 copies · chains A, B
- CL · Chloride 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 | 307 | 0.68 | 0.83 | 33 | GD, CL |
| 2 | 372 | 0.67 | 0.81 | 35 | GD, CL |
| 3 | 83 | 0.54 | 0.85 | 20 | empty |
| 4 | 54 | 0.39 | 0.81 | 14 | empty |
| 5 | 93 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 870 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3ZTY · The 3-dimensional structure of the gadolinium derivative of MpgP, the… · 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 Q72K29
- Elsewhere: RCSB PDB 3ZTY · PDBe 3ZTY · UniProt Q72K29
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