Research workbench
The 3-dimensional structure of mpgp from thermus thermophilus HB27, in complex with the alpha-mannosylglycerate and orthophosphate reaction products.
Analyse The 3-dimensional structure of mpgp from thermus thermophilus HB27, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZUP
- Type
- protein
- Length
- 506 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
- 2M8, MG, PO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 253 | 43% helix, 19% strand | Q72K29 |
Ligands and binding sites
- 2M8 · (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.67 | 0.82 | 38 | MG, PO4, 2M8 |
| 2 | 310 | 0.64 | 0.80 | 32 | PO4, 2M8 |
| 3 | 192 | 0.61 | 0.82 | 35 | empty |
| 4 | 181 | 0.47 | 0.75 | 24 | empty |
| 5 | 105 | 0.39 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZUP · The 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with 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 3ZUP · PDBe 3ZUP · UniProt Q72K29
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