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The 3-dimensional structure of mpgp from thermus thermophilus HB27, in complex with the alpha-MANNOSYLGLYCERATE,ORTHOPHOSPHATE and magnesium
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
- 3ZX4
- Type
- protein
- Length
- 504 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
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 250 | 40% helix, 19% strand | Q72K29 |
| B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 254 | 41% helix, 20% 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
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 | 313 | 0.67 | 0.82 | 42 | MG, PO4, 2M8 |
| 2 | 284 | 0.64 | 0.81 | 40 | MG, PO4, 2M8 |
| 3 | 119 | 0.56 | 0.83 | 26 | empty |
| 4 | 141 | 0.46 | 0.77 | 23 | empty |
| 5 | 125 | 0.40 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 806 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZX4 · 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 3ZX4 · PDBe 3ZX4 · UniProt Q72K29
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