Research workbench
The 3-dimensional structure of mpgp from thermus thermophilus HB27, covalently bound to vanadate and in complex with alpha- mannosylglycerate and magnesium
Analyse The 3-dimensional structure of mpgp from thermus thermophilus HB27, covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZX5
- 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
- VN4, 2M8, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 251 | 40% helix, 21% strand | Q72K29 |
Ligands and binding sites
- VN4 · oxido(dioxo)vanadium · ligand · 2 copies · chains A, B
- 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
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 | 241 | 0.67 | 0.84 | 37 | MG, VN4, 2M8 |
| 2 | 259 | 0.66 | 0.83 | 38 | MG, VN4, 2M8 |
| 3 | 213 | 0.57 | 0.79 | 36 | empty |
| 4 | 135 | 0.44 | 0.76 | 21 | empty |
| 5 | 120 | 0.43 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 772 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZX5 · The 3-dimensional structure of MpgP from Thermus thermophilus HB27, covalently bound to… · 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 3ZX5 · PDBe 3ZX5 · UniProt Q72K29
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